In this paper, we study the graph-based semi-supervised learning for classifying nodes in attributed networks, where the nodes and edges possess content information. Recent approaches like graph convolution networks and attention mechanisms have been proposed to ensemble the first-order neighbors and incorporate the relevant neighbors. However, it is costly (especially in memory) to consider all neighbors without a prior differentiation. We propose to explore the neighborhood in a reinforcement learning setting and find a walk path well-tuned for classifying the unlabelled target nodes. We let an agent (of node classification task) walk over the graph and decide where to direct to maximize classification accuracy. We define the graph walk as a partially observable Markov decision process (POMDP). The proposed method is flexible for working in both transductive and inductive setting. Extensive experiments on four datasets demonstrate that our proposed method outperforms several state-of-the-art methods. Several case studies also illustrate the meaningful movement trajectory made by the agent.
Complex networks represented as node adjacency matrices constrains the application of machine learning and parallel algorithms. To address this limitation, network embedding (i.e., graph representation) has been intensively studied to learn a fixed-length vector for each node in an embedding space, where the node properties in the original graph are preserved. Existing methods mainly focus on learning embedding vectors to preserve nodes proximity, i.e., nodes next to each other in the graph space should also be closed in the embedding space, but do not enforce algebraic statistical properties to be shared between the embedding space and graph space. In this work, we propose a lightweight model, entitled Network2Vec, to learn network embedding on the base of semantic distance mapping between the graph space and embedding space. The model builds a bridge between the two spaces leveraging the property of group homomorphism. Experiments on different learning tasks, including node classification, link prediction, and community visualization, demonstrate the effectiveness and efficiency of the new embedding method, which improves the state-of-the-art model by 19% in node classification and 7% in link prediction tasks at most. In addition, our method is significantly faster, consuming only a fraction of the time used by some famous methods.
In this work, we study semi-supervised multi-label node classification problem in attributed graphs. Classic solutions to multi-label node classification follow two steps, first learn node embedding and then build a node classifier on the learned embedding. To improve the discriminating power of the node embedding, we propose a novel collaborative graph walk, named Multi-Label-Graph-Walk, to finely tune node representations with the available label assignments in attributed graphs via reinforcement learning. The proposed method formulates the multi-label node classification task as simultaneous graph walks conducted by multiple label-specific agents. Furthermore, policies of the label-wise graph walks are learned in a cooperative way to capture first the predictive relation between node labels and structural attributes of graphs; and second, the correlation among the multiple label-specific classification tasks. A comprehensive experimental study demonstrates that the proposed method can achieve significantly better multi-label classification performance than the state-of-the-art approaches and conduct more efficient graph exploration.
Graph Neural Networks (GNNs) for prediction tasks like node classification or edge prediction have received increasing attention in recent machine learning from graphically structured data. However, a large quantity of labeled graphs is difficult to obtain, which significantly limits the true success of GNNs. Although active learning has been widely studied for addressing label-sparse issues with other data types like text, images, etc., how to make it effective over graphs is an open question for research. In this paper, we present an investigation on active learning with GNNs for node classification tasks. Specifically, we propose a new method, which uses node feature propagation followed by K-Medoids clustering of the nodes for instance selection in active learning. With a theoretical bound analysis we justify the design choice of our approach. In our experiments on four benchmark datasets, the proposed method outperforms other representative baseline methods consistently and significantly.
Convolutional Neural Networks (CNNs) have been very successful at solving a variety of computer vision tasks such as object classification and detection, semantic segmentation, activity understanding, to name just a few. One key enabling factor for their great performance has been the ability to train very deep networks. Despite their huge success in many tasks, CNNs do not work well with non-Euclidean data, which is prevalent in many real-world applications. Graph Convolutional Networks (GCNs) offer an alternative that allows for non-Eucledian data input to a neural network. While GCNs already achieve encouraging results, they are currently limited to architectures with a relatively small number of layers, primarily due to vanishing gradients during training. This work transfers concepts such as residual/dense connections and dilated convolutions from CNNs to GCNs in order to successfully train very deep GCNs. We show the benefit of using deep GCNs (with as many as 112 layers) experimentally across various datasets and tasks. Specifically, we achieve very promising performance in part segmentation and semantic segmentation on point clouds and in node classification of protein functions across biological protein-protein interaction (PPI) graphs. We believe that the insights in this work will open avenues for future research on GCNs and their application to further tasks not explored in this paper. The source code for this work is available at https://github.com/lightaime/deep_gcns_torch and https://github.com/lightaime/deep_gcns for PyTorch and TensorFlow implementation respectively.
Link prediction aims to infer missing links or predicting the future ones based on currently observed partial networks, it is a fundamental problem in network science with tremendous real-world applications. However, conventional link prediction approaches neither have high prediction accuracy nor being capable of revealing the hidden information behind links. To address this problem, we generalize the latest techniques in deep learning on graphs and present a new link prediction model - DeepLinker. Instead of learning node representation with the node label information, DeepLinker uses the links as supervised information. Experiments on five graphs show that DeepLinker can not only achieve the state-of-the-art link prediction accuracy, but also acquire the efficient node representations and node centrality ranking as the byproducts. Although the representations are obtained without any supervised node label information, they still perform well on node ranking and node classification tasks.
Towards the challenging problem of semi-supervised node classification, there have been extensive studies. As a frontier, Graph Neural Networks (GNNs) have aroused great interest recently, which update the representation of each node by aggregating information of its neighbors. However, most GNNs have shallow layers with a limited receptive field and may not achieve satisfactory performance especially when the number of labeled nodes is quite small. To address this challenge, we innovatively propose a graph few-shot learning (GFL) algorithm that incorporates prior knowledge learned from auxiliary graphs to improve classification accuracy on the target graph. Specifically, a transferable metric space characterized by a node embedding and a graph-specific prototype embedding function is shared between auxiliary graphs and the target, facilitating the transfer of structural knowledge. Extensive experiments and ablation studies on four real-world graph datasets demonstrate the effectiveness of our proposed model.
Textual network embedding aims to learn low-dimensional representations of text-annotated nodes in a graph. Prior work in this area has typically focused on fixed graph structures; however, real-world networks are often dynamic. We address this challenge with a novel end-to-end node-embedding model, called Dynamic Embedding for Textual Networks with a Gaussian Process (DetGP). After training, DetGP can be applied efficiently to dynamic graphs without re-training or backpropagation. The learned representation of each node is a combination of textual and structural embeddings. Because the structure is allowed to be dynamic, our method uses the Gaussian process to take advantage of its non-parametric properties. To use both local and global graph structures, diffusion is used to model multiple hops between neighbors. The relative importance of global versus local structure for the embeddings is learned automatically. With the non-parametric nature of the Gaussian process, updating the embeddings for a changed graph structure requires only a forward pass through the learned model. Considering link prediction and node classification, experiments demonstrate the empirical effectiveness of our method compared to baseline approaches. We further show that DetGP can be straightforwardly and efficiently applied to dynamic textual networks.
From social networks to protein complexes to disease genomes to visual data, hypergraphs are everywhere. However, the scope of research studying deep learning on hypergraphs is still quite sparse and nascent, as there has not yet existed an effective, unified framework for using hyperedge and vertex embeddings jointly in the hypergraph context, despite a large body of prior work that has shown the utility of deep learning over graphs and sets. Building upon these recent advances, we propose \textit{Deep Hyperedges} (DHE), a modular framework that jointly uses contextual and permutation-invariant vertex membership properties of hyperedges in hypergraphs to perform classification and regression in transductive and inductive learning settings. In our experiments, we use a novel random walk procedure and show that our model achieves and, in most cases, surpasses state-of-the-art performance on benchmark datasets. Additionally, we study our framework's performance on a variety of diverse, non-standard hypergraph datasets and propose several avenues of future work to further enhance DHE.
Graph kernels are kernel methods measuring graph similarity and serve as a standard tool for graph classification. However, the use of kernel methods for node classification, which is a related problem to graph representation learning, is still ill-posed and the state-of-the-art methods are heavily based on heuristics. Here, we present a novel theoretical kernel-based framework for node classification that can bridge the gap between these two representation learning problems on graphs. Our approach is motivated by graph kernel methodology but extended to learn the node representations capturing the structural information in a graph. We theoretically show that our formulation is as powerful as any positive semidefinite kernels. To efficiently learn the kernel, we propose a novel mechanism for node feature aggregation and a data-driven similarity metric employed during the training phase. More importantly, our framework is flexible and complementary to other graph-based deep learning models, e.g., Graph Convolutional Networks (GCNs). We empirically evaluate our approach on a number of standard node classification benchmarks, and demonstrate that our model sets the new state of the art.
Graph neural networks (GNNs) are designed for semi-supervised node classification on graphs where only a subset of nodes have class labels. However, under extreme cases when very few labels are available (e.g., 1 labeled node per class), GNNs suffer from severe performance degradation. Specifically, we observe that existing GNNs suffer from unstable training process on few-labeled graphs, resulting to inferior performance on node classification. Therefore, we propose an effective framework, Stabilized Self-Training (SST), which is applicable to existing GNNs to handle the scarcity of labeled data, and consequently, boost classification accuracy. We conduct thorough empirical and theoretical analysis to support our findings and motivate the algorithmic designs in SST. We apply SST to two popular GNN models GCN and DAGNN, to get SSTGCN and SSTDA methods respectively, and evaluate the two methods against 10 competitors over 5 benchmarking datasets. Extensive experiments show that the proposed SST framework is highly effective, especially when few labeled data are available. Our methods achieve superior performance under almost all settings over all datasets. For instance, on a Cora dataset with only 1 labeled node per class, the accuracy of SSTGCN is 62.5%, 17.9% higher than GCN, and the accuracy of SSTDA is 66.4%, which outperforms DAGNN by 6.6%.
Learning network representations is a fundamental task for many graph applications such as link prediction, node classification, graph clustering, and graph visualization. Many real-world networks are interpreted as dynamic networks and evolve over time. Most existing graph embedding algorithms were developed for static graphs mainly and cannot capture the evolution of a large dynamic network. In this paper, we propose Dynamic joint Variational Graph Autoencoders (Dyn-VGAE) that can learn both local structures and temporal evolutionary patterns in a dynamic network. Dyn-VGAE provides a joint learning framework for computing temporal representations of all graph snapshots simultaneously. Each auto-encoder embeds a graph snapshot based on its local structure and can also learn temporal dependencies by collaborating with other autoencoders. We conduct experimental studies on dynamic real-world graph datasets and the results demonstrate the effectiveness of the proposed method.
Graph representation learning, aiming to learn low-dimensional representations which capture the geometric dependencies between nodes in the original graph, has gained increasing popularity in a variety of graph analysis tasks, including node classification and link prediction. Existing representation learning methods based on graph neural networks and their variants rely on the aggregation of neighborhood information, which makes it sensitive to noises in the graph. In this paper, we propose Graph Denoising Policy Network (short for GDPNet) to learn robust representations from noisy graph data through reinforcement learning. GDPNet first selects signal neighborhoods for each node, and then aggregates the information from the selected neighborhoods to learn node representations for the down-stream tasks. Specifically, in the signal neighborhood selection phase, GDPNet optimizes the neighborhood for each target node by formulating the process of removing noisy neighborhoods as a Markov decision process and learning a policy with task-specific rewards received from the representation learning phase. In the representation learning phase, GDPNet aggregates features from signal neighbors to generate node representations for down-stream tasks, and provides task-specific rewards to the signal neighbor selection phase. These two phases are jointly trained to select optimal sets of neighbors for target nodes with maximum cumulative task-specific rewards, and to learn robust representations for nodes. Experimental results on node classification task demonstrate the effectiveness of GDNet, outperforming the state-of-the-art graph representation learning methods on several well-studied datasets. Additionally, GDPNet is mathematically equivalent to solving the submodular maximizing problem, which theoretically guarantees the best approximation to the optimal solution with GDPNet.
This work provides the first unifying theoretical framework for node (positional) embeddings and structural graph representations, bridging methods like matrix factorization and graph neural networks. Using invariant theory, we show that the relationship between structural representations and node embeddings is analogous to that of a distribution and its samples. We prove that all tasks that can be performed by node embeddings can also be performed by structural representations and vice-versa. We also show that the concept of transductive and inductive learning is unrelated to node embeddings and graph representations, clearing another source of confusion in the literature. Finally, we introduce new practical guidelines to generating and using node embeddings, which fixes significant shortcomings of standard operating procedures used today.
Graph node embedding aims at learning a vector representation for all nodes given a graph. It is a central problem in many machine learning tasks (e.g., node classification, recommendation, community detection). The key problem in graph node embedding lies in how to define the dependence to neighbors. Existing approaches specify (either explicitly or implicitly) certain dependencies on neighbors, which may lead to loss of subtle but important structural information within the graph and other dependencies among neighbors. This intrigues us to ask the question: can we design a model to give the maximal flexibility of dependencies to each node's neighborhood. In this paper, we propose a novel graph node embedding (named PINE) via a novel notion of partial permutation invariant set function, to capture any possible dependence. Our method 1) can learn an arbitrary form of the representation function from the neighborhood, withour losing any potential dependence structures, and 2) is applicable to both homogeneous and heterogeneous graph embedding, the latter of which is challenged by the diversity of node types. Furthermore, we provide theoretical guarantee for the representation capability of our method for general homogeneous and heterogeneous graphs. Empirical evaluation results on benchmark data sets show that our proposed PINE method outperforms the state-of-the-art approaches on producing node vectors for various learning tasks of both homogeneous and heterogeneous graphs.
We present GraphMix, a regularization method for Graph Neural Network based semi-supervised object classification, whereby we propose to train a fully-connected network jointly with the graph neural network via parameter sharing and interpolation-based regularization. Further, we provide a theoretical analysis of how GraphMix improves the generalization bounds of the underlying graph neural network, without making any assumptions about the "aggregation" layer or the depth of the graph neural networks. We experimentally validate this analysis by applying GraphMix to various architectures such as Graph Convolutional Networks, Graph Attention Networks and Graph-U-Net. Despite its simplicity, we demonstrate that GraphMix can consistently improve or closely match state-of-the-art performance using even simpler architectures such as Graph Convolutional Networks, across three established graph benchmarks: Cora, Citeseer and Pubmed citation network datasets, as well as three newly proposed datasets: Cora-Full, Co-author-CS and Co-author-Physics.
Graph convolutional neural networks (GCN) have been the model of choice for graph representation learning, which is mainly due to the effective design of graph convolution that computes the representation of a node by aggregating those of its neighbors. However, existing GCN variants commonly use 1-D graph convolution that solely operates on the object link graph without exploring informative relational information among object attributes. This significantly limits their modeling capability and may lead to inferior performance on noisy and sparse real-world networks. In this paper, we explore 2-D graph convolution to jointly model object links and attribute relations for graph representation learning. Specifically, we propose a computationally efficient dimensionwise separable 2-D graph convolution (DSGC) for filtering node features. Theoretically, we show that DSGC can reduce intra-class variance of node features on both the object dimension and the attribute dimension to learn more effective representations. Empirically, we demonstrate that by modeling attribute relations, DSGC achieves significant performance gain over state-of-the-art methods for node classification and clustering on a variety of real-world networks. The source code for reproducing the experimental results is available at https://github.com/liqimai/DSGC.
Real-world graph applications, such as advertisements and product recommendations make profits based on accurately classify the label of the nodes. However, in such scenarios, there are high incentives for the adversaries to attack such graph to reduce the node classification performance. Previous work on graph adversarial attacks focus on modifying existing graph structures, which is infeasible in most real-world applications. In contrast, it is more practical to inject adversarial nodes into existing graphs, which can also potentially reduce the performance of the classifier. In this paper, we study the novel node injection poisoning attacks problem which aims to poison the graph. We describe a reinforcement learning based method, namely NIPA, to sequentially modify the adversarial information of the injected nodes. We report the results of experiments using several benchmark data sets that show the superior performance of the proposed method NIPA, relative to the existing state-of-the-art methods.
The existing graph neural networks (GNNs) based on the spectral graph convolutional operator have been criticized for its performance degradation, which is especially common for the models with deep architectures. In this paper, we further identify the suspended animation problem with the existing GNNs. Such a problem happens when the model depth reaches the suspended animation limit, and the model will not respond to the training data any more and become not learnable. Analysis about the causes of the suspended animation problem with existing GNNs will be provided in this paper, whereas several other peripheral factors that will impact the problem will be reported as well. To resolve the problem, we introduce the GResNet (Graph Residual Network) framework in this paper, which creates extensively connected highways to involve nodes' raw features or intermediate representations throughout the graph for all the model layers. Different from the other learning settings, the extensive connections in the graph data will render the existing simple residual learning methods fail to work. We prove the effectiveness of the introduced new graph residual terms from the norm preservation perspective, which will help avoid dramatic changes to the node's representations between sequential layers. Detailed studies about the GResNet framework for many existing GNNs, including GCN, GAT and LoopyNet, will be reported in the paper with extensive empirical experiments on real-world benchmark datasets.
Graph neural networks (GNN) has been successfully applied to operate on the graph-structured data. Given a specific scenario, rich human expertise and tremendous laborious trials are usually required to identify a suitable GNN architecture. It is because the performance of a GNN architecture is significantly affected by the choice of graph convolution components, such as aggregate function and hidden dimension. Neural architecture search (NAS) has shown its potential in discovering effective deep architectures for learning tasks in image and language modeling. However, existing NAS algorithms cannot be directly applied to the GNN search problem. First, the search space of GNN is different from the ones in existing NAS work. Second, the representation learning capacity of GNN architecture changes obviously with slight architecture modifications. It affects the search efficiency of traditional search methods. Third, widely used techniques in NAS such as parameter sharing might become unstable in GNN. To bridge the gap, we propose the automated graph neural networks (AGNN) framework, which aims to find an optimal GNN architecture within a predefined search space. A reinforcement learning based controller is designed to greedily validate architectures via small steps. AGNN has a novel parameter sharing strategy that enables homogeneous architectures to share parameters, based on a carefully-designed homogeneity definition. Experiments on real-world benchmark datasets demonstrate that the GNN architecture identified by AGNN achieves the best performance, comparing with existing handcrafted models and tradistional search methods.