Graph convolutional networks (GCNs) have achieved great success on graph-structured data. Many graph convolutional networks can be thought of as low-pass filters for graph signals. In this paper, we propose a more powerful graph convolutional network, named BiGCN, that extends to bidirectional filtering. Specifically, we not only consider the original graph structure information but also the latent correlation between features, thus BiGCN can filter the signals along with both the original graph and a latent feature-connection graph. Compared with most existing GCNs, BiGCN is more robust and has powerful capacities for feature denoising. We perform node classification and link prediction in citation networks and co-purchase networks with three settings: noise-rate, noise-level and structure-mistakes. Extensive experimental results demonstrate that our model outperforms the state-of-the-art graph neural networks in both clean and artificially noisy data.
In this paper, we study how to simultaneously learn two highly correlated tasks of graph analysis, i.e., community detection and node representation learning. We propose an efficient generative model called VECoDeR for jointly learning Variational Embeddings for Community Detection and node Representation. VECoDeR assumes that every node can be a member of one or more communities. The node embeddings are learned in such a way that connected nodes are not only "closer" to each other but also share similar community assignments. A joint learning framework leverages community-aware node embeddings for better community detection. We demonstrate on several graph datasets that VECoDeR effectively out-performs many competitive baselines on all three tasks i.e. node classification, overlapping community detection and non-overlapping community detection. We also show that VECoDeR is computationally efficient and has quite robust performance with varying hyperparameters.
Proximity preserving and structural role-based node embeddings have become a prime workhorse of applied graph mining. Novel node embedding techniques are often tested on a restricted set of benchmark datasets. In this paper, we propose a new diverse social network dataset called Twitch Gamers with multiple potential target attributes. Our analysis of the social network and node classification experiments illustrate that Twitch Gamers is suitable for assessing the predictive performance of novel proximity preserving and structural role-based node embedding algorithms.
A scalable semi-supervised node classification method on graph-structured data, called GraphHop, is proposed in this work. The graph contains attributes of all nodes but labels of a few nodes. The classical label propagation (LP) method and the emerging graph convolutional network (GCN) are two popular semi-supervised solutions to this problem. The LP method is not effective in modeling node attributes and labels jointly or facing a slow convergence rate on large-scale graphs. GraphHop is proposed to its shortcoming. With proper initial label vector embeddings, each iteration of GraphHop contains two steps: 1) label aggregation and 2) label update. In Step 1, each node aggregates its neighbors' label vectors obtained in the previous iteration. In Step 2, a new label vector is predicted for each node based on the label of the node itself and the aggregated label information obtained in Step 1. This iterative procedure exploits the neighborhood information and enables GraphHop to perform well in an extremely small label rate setting and scale well for very large graphs. Experimental results show that GraphHop outperforms state-of-the-art graph learning methods on a wide range of tasks (e.g., multi-label and multi-class classification on citation networks, social graphs, and commodity consumption graphs) in graphs of various sizes. Our codes are publicly available on GitHub (https://github.com/TianXieUSC/GraphHop).
Embedding static graphs in low-dimensional vector spaces plays a key role in network analytics and inference, supporting applications like node classification, link prediction, and graph visualization. However, many real-world networks present dynamic behavior, including topological evolution, feature evolution, and diffusion. Therefore, several methods for embedding dynamic graphs have been proposed to learn network representations over time, facing novel challenges, such as time-domain modeling, temporal features to be captured, and the temporal granularity to be embedded. In this survey, we overview dynamic graph embedding, discussing its fundamentals and the recent advances developed so far. We introduce the formal definition of dynamic graph embedding, focusing on the problem setting and introducing a novel taxonomy for dynamic graph embedding input and output. We further explore different dynamic behaviors that may be encompassed by embeddings, classifying by topological evolution, feature evolution, and processes on networks. Afterward, we describe existing techniques and propose a taxonomy for dynamic graph embedding techniques based on algorithmic approaches, from matrix and tensor factorization to deep learning, random walks, and temporal point processes. We also elucidate main applications, including dynamic link prediction, anomaly detection, and diffusion prediction, and we further state some promising research directions in the area.
Graphs are often used to organize data because of their simple topological structure, and therefore play a key role in machine learning. And it turns out that the low-dimensional embedded representation obtained by graph representation learning are extremely useful in various typical tasks, such as node classification, content recommendation and link prediction. However, the existing methods mostly start from the microstructure (i.e., the edges) in the graph, ignoring the mesoscopic structure (high-order local structure). Here, we propose wGCN -- a novel framework that utilizes random walk to obtain the node-specific mesoscopic structures of the graph, and utilizes these mesoscopic structures to reconstruct the graph And organize the characteristic information of the nodes. Our method can effectively generate node embeddings for previously unseen data, which has been proven in a series of experiments conducted on citation networks and social networks (our method has advantages over baseline methods). We believe that combining high-order local structural information can more efficiently explore the potential of the network, which will greatly improve the learning efficiency of graph neural network and promote the establishment of new learning models.
Heterogeneous graphs generally refers to graphs with different types of nodes and edges. A common approach for extracting useful information from heterogeneous graphs is to use meta-graphs, which can be seen as a special kind of directed acyclic graph (DAG) with same node and edge types as the heterogeneous graph. However, how to design proper meta-graphs is challenging. Recently, there have been many works on learning suitable meta-graphs from a heterogeneous graph. Existing methods generally introduce continuous weights for edges that are independent of each other, which ignores the topological stucture of meta-graphs and can be ineffective. To address this issue, we propose a new viewpoint from tensor on learning meta-graphs. Such a viewpoint not only helps interpret the limitation of existing works by CANDECOMP/PARAFAC (CP) decomposition, but also inspires us to propose a topology-aware tensor decomposition, called TENSUS, that reflects the structure of DAGs. The proposed topology-aware tensor decomposition is easy to use and simple to implement, and it can be taken as a plug-in part to upgrade many existing works, including node classification and recommendation on heterogeneous graphs. Experimental results on different tasks demonstrate that the proposed method can significantly improve the state-of-the-arts for all these tasks.
Graph neural networks (GNNs) have been proven to be effective in various network-related tasks. Most existing GNNs usually exploit the low-frequency signals of node features, which gives rise to one fundamental question: is the low-frequency information all we need in the real world applications? In this paper, we first present an experimental investigation assessing the roles of low-frequency and high-frequency signals, where the results clearly show that exploring low-frequency signal only is distant from learning an effective node representation in different scenarios. How can we adaptively learn more information beyond low-frequency information in GNNs? A well-informed answer can help GNNs enhance the adaptability. We tackle this challenge and propose a novel Frequency Adaptation Graph Convolutional Networks (FAGCN) with a self-gating mechanism, which can adaptively integrate different signals in the process of message passing. For a deeper understanding, we theoretically analyze the roles of low-frequency signals and high-frequency signals on learning node representations, which further explains why FAGCN can perform well on different types of networks. Extensive experiments on six real-world networks validate that FAGCN not only alleviates the over-smoothing problem, but also has advantages over the state-of-the-arts.
In the quest to improve efficiency, interdependence and complexity are becoming defining characteristics of modern complex networks representing engineered and natural systems. Graph theory is a widely used framework for modeling such complex networks and to evaluate their robustness to disruptions. Particularly, identification of critical nodes/links in a graph can facilitate the enhancement of graph (system) robustness and characterize crucial factors of system performance. Most existing methods of critical node identification are based on an iterative approach that explores each node/link of a graph. These methods suffer from high computational complexity and the resulting analysis is network specific. Additionally, uncertainty associated with the underlying graphical model further limits the potential value of these traditional approaches. To overcome these challenges, we propose a Bayesian graph neural network based node classification framework that is computationally efficient and systematically incorporates uncertainties. Instead of utilizing the observed graph for training the model, a MAP estimate of the graph is computed based on the observed topology and node target labels. Further, a Monte-Carlo (MC) dropout algorithm is incorporated to account for the epistemic uncertainty. The fidelity and the gain in computational complexity offered by the Bayesian framework is illustrated using simulation results.
Graph Neural Networks (GNNs) have received much attention in the graph deep learning domain. However, recent research empirically and theoretically shows that deep GNNs suffer from over-fitting and over-smoothing problems. The usual solutions either cannot solve extensive runtime of deep GNNs or restrict graph convolution in the same feature space. We propose the Adaptive Graph Diffusion Networks (AGDNs) which perform multi-layer generalized graph diffusion in different feature spaces with moderate complexity and runtime. Standard graph diffusion methods combine large and dense powers of the transition matrix with predefined weighting coefficients. Instead, AGDNs combine smaller multi-hop node representations with learnable and generalized weighting coefficients. We propose two scalable mechanisms of weighting coefficients to capture multi-hop information: Hop-wise Attention (HA) and Hop-wise Convolution (HC). We evaluate AGDNs on diverse, challenging Open Graph Benchmark (OGB) datasets with semi-supervised node classification and link prediction tasks. Until the date of submission (Aug 26, 2022), AGDNs achieve top-1 performance on the ogbn-arxiv, ogbn-proteins and ogbl-ddi datasets and top-3 performance on the ogbl-citation2 dataset. On the similar Tesla V100 GPU cards, AGDNs outperform Reversible GNNs (RevGNNs) with 13% complexity and 1% training runtime of RevGNNs on the ogbn-proteins dataset. AGDNs also achieve comparable performance to SEAL with 36% training and 0.2% inference runtime of SEAL on the ogbl-citation2 dataset.
Semi-supervised node classification on graph-structured data has many applications such as fraud detection, fake account and review detection, user's private attribute inference in social networks, and community detection. Various methods such as pairwise Markov Random Fields (pMRF) and graph neural networks were developed for semi-supervised node classification. pMRF is more efficient than graph neural networks. However, existing pMRF-based methods are less accurate than graph neural networks, due to a key limitation that they assume a heuristics-based constant edge potential for all edges. In this work, we aim to address the key limitation of existing pMRF-based methods. In particular, we propose to learn edge potentials for pMRF. Our evaluation results on various types of graph datasets show that our optimized pMRF-based method consistently outperforms existing graph neural networks in terms of both accuracy and efficiency. Our results highlight that previous work may have underestimated the power of pMRF for semi-supervised node classification.
Higher-order proximity (HOP) is fundamental for most network embedding methods due to its significant effects on the quality of node embedding and performance on downstream network analysis tasks. Most existing HOP definitions are based on either homophily to place close and highly interconnected nodes tightly in embedding space or heterophily to place distant but structurally similar nodes together after embedding. In real-world networks, both can co-exist, and thus considering only one could limit the prediction performance and interpretability. However, there is no general and universal solution that takes both into consideration. In this paper, we propose such a simple yet powerful framework called homophily and heterophliy preserving network transformation (H2NT) to capture HOP that flexibly unifies homophily and heterophily. Specifically, H2NT utilises motif representations to transform a network into a new network with a hybrid assumption via micro-level and macro-level walk paths. H2NT can be used as an enhancer to be integrated with any existing network embedding methods without requiring any changes to latter methods. Because H2NT can sparsify networks with motif structures, it can also improve the computational efficiency of existing network embedding methods when integrated. We conduct experiments on node classification, structural role classification and motif prediction to show the superior prediction performance and computational efficiency over state-of-the-art methods. In particular, DeepWalk-based H2 NT achieves 24% improvement in terms of precision on motif prediction, while reducing 46% computational time compared to the original DeepWalk.
Graph neural networks (GNNs) have been investigated for potential applicability in multiple fields that employ graph data. However, there are no standard training settings to ensure fair comparisons among new methods, including different model architectures and data augmentation techniques. We introduce a standard, reproducible benchmark to which the same training settings can be applied for node classification. For this benchmark, we constructed 9 datasets, including both small- and medium-scale datasets from different fields, and 7 different models. We design a k-fold model assessment strategy for small datasets and a standard set of model training procedures for all datasets, enabling a standard experimental pipeline for GNNs to help ensure fair model architecture comparisons. We use node2vec and Laplacian eigenvectors to perform data augmentation to investigate how input features affect the performance of the models. We find topological information is important for node classification tasks. Increasing the number of model layers does not improve the performance except on the PATTERN and CLUSTER datasets, in which the graphs are not connected. Data augmentation is highly useful, especially using node2vec in the baseline, resulting in a substantial baseline performance improvement.
Spectral graph convolutional networks are generalizations of standard convolutional networks for graph-structured data using the Laplacian operator. A common misconception is the instability of spectral filters, i.e. the impossibility to transfer spectral filters between graphs of variable size and topology. This misbelief has limited the development of spectral networks for multi-graph tasks in favor of spatial graph networks. However, recent works have proved the stability of spectral filters under graph perturbation. Our work complements and emphasizes further the high quality of spectral transferability by benchmarking spectral graph networks on tasks involving graphs of different size and connectivity. Numerical experiments exhibit favorable performance on graph regression, graph classification, and node classification problems on two graph benchmarks. The implementation of our experiments is available on GitHub for reproducibility.
We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.
Expressivity plays a fundamental role in evaluating deep neural networks, and it is closely related to understanding the limit of performance improvement. In this paper, we propose a three-pipeline training framework based on critical expressivity, including global model contraction, weight evolution, and link's weight rewiring. Specifically, we propose a pyramidal-like skeleton to overcome the saddle points that affect information transfer. Then we analyze the reason for the modularity (clustering) phenomenon in network topology and use it to rewire potential erroneous weighted links. We conduct numerical experiments on node classification and the results confirm that the proposed training framework leads to a significantly improved performance in terms of fast convergence and robustness to potential erroneous weighted links. The architecture design on GNNs, in turn, verifies the expressivity of GNNs from dynamics and topological space aspects and provides useful guidelines in designing more efficient neural networks.
Graph neural networks (GNNs) extend convolutional neural networks (CNNs) to graph-based data. A question that arises is how much performance improvement does the underlying graph structure in the GNN provide over the CNN (that ignores this graph structure). To address this question, we introduce edge entropy and evaluate how good an indicator it is for possible performance improvement of GNNs over CNNs. Our results on node classification with synthetic and real datasets show that lower values of edge entropy predict larger expected performance gains of GNNs over CNNs, and, conversely, higher edge entropy leads to expected smaller improvement gains.
Graph analytics can lead to better quantitative understanding and control of complex networks, but traditional methods suffer from high computational cost and excessive memory requirements associated with the high-dimensionality and heterogeneous characteristics of industrial size networks. Graph embedding techniques can be effective in converting high-dimensional sparse graphs into low-dimensional, dense and continuous vector spaces, preserving maximally the graph structure properties. Another type of emerging graph embedding employs Gaussian distribution-based graph embedding with important uncertainty estimation. The main goal of graph embedding methods is to pack every node's properties into a vector with a smaller dimension, hence, node similarity in the original complex irregular spaces can be easily quantified in the embedded vector spaces using standard metrics. The generated nonlinear and highly informative graph embeddings in the latent space can be conveniently used to address different downstream graph analytics tasks (e.g., node classification, link prediction, community detection, visualization, etc.). In this Review, we present some fundamental concepts in graph analytics and graph embedding methods, focusing in particular on random walk-based and neural network-based methods. We also discuss the emerging deep learning-based dynamic graph embedding methods. We highlight the distinct advantages of graph embedding methods in four diverse applications, and present implementation details and references to open-source software as well as available databases in the Appendix for the interested readers to start their exploration into graph analytics.
Graph Contrastive Learning (GCL) has proven highly effective in promoting the performance of Semi-Supervised Node Classification (SSNC). However, existing GCL methods are generally transferred from other fields like CV or NLP, whose underlying working mechanism remains under-explored. In this work, we first deeply probe the working mechanism of GCL in SSNC, and find that the promotion brought by GCL is severely unevenly distributed: the improvement mainly comes from subgraphs with less annotated information, which is fundamentally different from contrastive learning in other fields. However, existing GCL methods generally ignore this uneven distribution of annotated information and apply GCL evenly to the whole graph. To remedy this issue and further improve GCL in SSNC, we propose the Topology InFormation gain-Aware Graph Contrastive Learning (TIFA-GCL) framework that considers the annotated information distribution across graph in GCL. Extensive experiments on six benchmark graph datasets, including the enormous OGB-Products graph, show that TIFA-GCL can bring a larger improvement than existing GCL methods in both transductive and inductive settings. Further experiments demonstrate the generalizability and interpretability of TIFA-GCL.
Node classification on graphs is an important task in many practical domains. It usually requires labels for training, which can be difficult or expensive to obtain in practice. Given a budget for labelling, active learning aims to improve performance by carefully choosing which nodes to label. Previous graph active learning methods learn representations using labelled nodes and select some unlabelled nodes for label acquisition. However, they do not fully utilize the representation power present in unlabelled nodes. We argue that the representation power in unlabelled nodes can be useful for active learning and for further improving performance of active learning for node classification. In this paper, we propose a latent space clustering-based active learning framework for node classification (LSCALE), where we fully utilize the representation power in both labelled and unlabelled nodes. Specifically, to select nodes for labelling, our framework uses the K-Medoids clustering algorithm on a latent space based on a dynamic combination of both unsupervised features and supervised features. In addition, we design an incremental clustering module to avoid redundancy between nodes selected at different steps. Extensive experiments on five datasets show that our proposed framework LSCALE consistently and significantly outperforms the stateof-the-art approaches by a large margin.