As an efficient and scalable graph neural network, GraphSAGE has enabled an inductive capability for inferring unseen nodes or graphs by aggregating subsampled local neighborhoods and by learning in a mini-batch gradient descent fashion. The neighborhood sampling used in GraphSAGE is effective in order to improve computing and memory efficiency when inferring a batch of target nodes with diverse degrees in parallel. Despite this advantage, the default uniform sampling suffers from high variance in training and inference, leading to sub-optimum accuracy. We propose a new data-driven sampling approach to reason about the real-valued importance of a neighborhood by a non-linear regressor, and to use the value as a criterion for subsampling neighborhoods. The regressor is learned using a value-based reinforcement learning. The implied importance for each combination of vertex and neighborhood is inductively extracted from the negative classification loss output of GraphSAGE. As a result, in an inductive node classification benchmark using three datasets, our method enhanced the baseline using the uniform sampling, outperforming recent variants of a graph neural network in accuracy.
Graph Convolutional Representation (GCR) has achieved impressive performance for graph data representation. However, existing GCR is generally defined on the input fixed graph which may restrict the representation capacity and also be vulnerable to the structural attacks and noises. To address this issue, we propose a novel Latent Graph Convolutional Representation (LatGCR) for robust graph data representation and learning. Our LatGCR is derived based on reformulating graph convolutional representation from the aspect of graph neighborhood reconstruction. Given an input graph $\textbf{A}$, LatGCR aims to generate a flexible latent graph $\widetilde{\textbf{A}}$ for graph convolutional representation which obviously enhances the representation capacity and also performs robustly w.r.t graph structural attacks and noises. Moreover, LatGCR is implemented in a self-supervised manner and thus provides a basic block for both supervised and unsupervised graph learning tasks. Experiments on several datasets demonstrate the effectiveness and robustness of LatGCR.
Graph Neural Networks (GNNs) have been popularly used for analyzing non-Euclidean data such as social network data and biological data. Despite their success, the design of graph neural networks requires a lot of manual work and domain knowledge. In this paper, we propose a Graph Neural Architecture Search method (GraphNAS for short) that enables automatic search of the best graph neural architecture based on reinforcement learning. Specifically, GraphNAS first uses a recurrent network to generate variable-length strings that describe the architectures of graph neural networks, and then trains the recurrent network with reinforcement learning to maximize the expected accuracy of the generated architectures on a validation data set. Extensive experimental results on node classification tasks in both transductive and inductive learning settings demonstrate that GraphNAS can achieve consistently better performance on the Cora, Citeseer, Pubmed citation network, and protein-protein interaction network. On node classification tasks, GraphNAS can design a novel network architecture that rivals the best human-invented architecture in terms of test set accuracy.
Graph Convolutional Neural Networks (GCNNs) are generalizations of CNNs to graph-structured data, in which convolution is guided by the graph topology. In many cases where graphs are unavailable, existing methods manually construct graphs or learn task-driven adaptive graphs. In this paper, we propose Graph Learning Neural Networks (GLNNs), which exploit the optimization of graphs (the adjacency matrix in particular) from both data and tasks. Leveraging on spectral graph theory, we propose the objective of graph learning from a sparsity constraint, properties of a valid adjacency matrix as well as a graph Laplacian regularizer via maximum a posteriori estimation. The optimization objective is then integrated into the loss function of the GCNN, which adapts the graph topology to not only labels of a specific task but also the input data. Experimental results show that our proposed GLNN outperforms state-of-the-art approaches over widely adopted social network datasets and citation network datasets for semi-supervised classification.
Network embedding has proved extremely useful in a variety of network analysis tasks such as node classification, link prediction, and network visualization. Almost all the existing network embedding methods learn to map the node IDs to their corresponding node embeddings. This design principle, however, hinders the existing methods from being applied in real cases. Node ID is not generalizable and, thus, the existing methods have to pay great effort in cold-start problem. The heterogeneous network usually requires extra work to encode node types, as node type is not able to be identified by node ID. Node ID carries rare information, resulting in the criticism that the existing methods are not robust to noise. To address this issue, we introduce Compositional Network Embedding, a general inductive network representation learning framework that generates node embeddings by combining node features based on the principle of compositionally. Instead of directly optimizing an embedding lookup based on arbitrary node IDs, we learn a composition function that infers node embeddings by combining the corresponding node attribute embeddings through a graph-based loss. For evaluation, we conduct the experiments on link prediction under four different settings. The results verified the effectiveness and generalization ability of compositional network embeddings, especially on unseen nodes.
The main approaches for node classification in graphs are information propagation and the association of the class of the node with external information. State of the art methods merge these approaches through Graph Convolutional Networks. We here use the association of topological features of the nodes with their class to predict this class. Moreover, combining topological information with information propagation improves classification accuracy on the standard CiteSeer and Cora paper classification task. Topological features and information propagation produce results almost as good as text-based classification, without no textual or content information. We propose to represent the topology and information propagation through a GCN with the neighboring training node classification as an input and the current node classification as output. Such a formalism outperforms state of the art methods.
Node classification and graph classification are two graph learning problems that predict the class label of a node and the class label of a graph respectively. A node of a graph usually represents a real-world entity, e.g., a user in a social network, or a protein in a protein-protein interaction network. In this work, we consider a more challenging but practically useful setting, in which a node itself is a graph instance. This leads to a hierarchical graph perspective which arises in many domains such as social network, biological network and document collection. For example, in a social network, a group of people with shared interests forms a user group, whereas a number of user groups are interconnected via interactions or common members. We study the node classification problem in the hierarchical graph where a `node' is a graph instance, e.g., a user group in the above example. As labels are usually limited in real-world data, we design two novel semi-supervised solutions named \underline{SE}mi-supervised gr\underline{A}ph c\underline{L}assification via \underline{C}autious/\underline{A}ctive \underline{I}teration (or SEAL-C/AI in short). SEAL-C/AI adopt an iterative framework that takes turns to build or update two classifiers, one working at the graph instance level and the other at the hierarchical graph level. To simplify the representation of the hierarchical graph, we propose a novel supervised, self-attentive graph embedding method called SAGE, which embeds graph instances of arbitrary size into fixed-length vectors. Through experiments on synthetic data and Tencent QQ group data, we demonstrate that SEAL-C/AI not only outperform competing methods by a significant margin in terms of accuracy/Macro-F1, but also generate meaningful interpretations of the learned representations.
We propose a dynamic neighborhood aggregation (DNA) procedure guided by (multi-head) attention for representation learning on graphs. In contrast to current graph neural networks which follow a simple neighborhood aggregation scheme, our DNA procedure allows for a selective and node-adaptive aggregation of neighboring embeddings of potentially differing locality. In order to avoid overfitting, we propose to control the channel-wise connections between input and output by making use of grouped linear projections. In a number of transductive node-classification experiments, we demonstrate the effectiveness of our approach.
Convolutional Neural Networks (CNNs) achieve impressive performance in a wide variety of fields. Their success benefited from a massive boost when very deep CNN models were able to be reliably trained. Despite their merits, CNNs fail to properly address problems with non-Euclidean data. To overcome this challenge, Graph Convolutional Networks (GCNs) build graphs to represent non-Euclidean data, borrow concepts from CNNs, and apply them in training. GCNs show promising results, but they are usually limited to very shallow models due to the vanishing gradient problem. As a result, most state-of-the-art GCN models are no deeper than 3 or 4 layers. In this work, we present new ways to successfully train very deep GCNs. We do this by borrowing concepts from CNNs, specifically residual/dense connections and dilated convolutions, and adapting them to GCN architectures. Extensive experiments show the positive effect of these deep GCN frameworks. Finally, we use these new concepts to build a very deep 56-layer GCN, and show how it significantly boosts performance (+3.7% mIoU over state-of-the-art) in the task of point cloud semantic segmentation. We believe that the community can greatly benefit from this work, as it opens up many opportunities for advancing GCN-based research.
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
In this work, we present a method for node embedding in temporal graphs. We propose an algorithm that learns the evolution of a temporal graph's nodes and edges over time and incorporates this dynamics in a temporal node embedding framework for different graph prediction tasks. We present a joint loss function that creates a temporal embedding of a node by learning to combine its historical temporal embeddings, such that it optimizes per given task (e.g., link prediction). The algorithm is initialized using static node embeddings, which are then aligned over the representations of a node at different time points, and eventually adapted for the given task in a joint optimization. We evaluate the effectiveness of our approach over a variety of temporal graphs for the two fundamental tasks of temporal link prediction and multi-label node classification, comparing to competitive baselines and algorithmic alternatives. Our algorithm shows performance improvements across many of the datasets and baselines and is found particularly effective for graphs that are less cohesive, with a lower clustering coefficient.
There has been appreciable progress in unsupervised network representation learning (UNRL) approaches over graphs recently with flexible random-walk approaches, new optimization objectives and deep architectures. However, there is no common ground for systematic comparison of embeddings to understand their behavior for different graphs and tasks. In this paper we theoretically group different approaches under a unifying framework and empirically investigate the effectiveness of different network representation methods. In particular, we argue that most of the UNRL approaches either explicitly or implicit model and exploit context information of a node. Consequently, we propose a framework that casts a variety of approaches -- random walk based, matrix factorization and deep learning based -- into a unified context-based optimization function. We systematically group the methods based on their similarities and differences. We study the differences among these methods in detail which we later use to explain their performance differences (on downstream tasks). We conduct a large-scale empirical study considering 9 popular and recent UNRL techniques and 11 real-world datasets with varying structural properties and two common tasks -- node classification and link prediction. We find that there is no single method that is a clear winner and that the choice of a suitable method is dictated by certain properties of the embedding methods, task and structural properties of the underlying graph. In addition we also report the common pitfalls in evaluation of UNRL methods and come up with suggestions for experimental design and interpretation of results.
In a graph convolutional network, we assume that the graph $G$ is generated wrt some observation noise. During learning, we make small random perturbations $\Delta{}G$ of the graph and try to improve generalization. Based on quantum information geometry, $\Delta{}G$ can be characterized by the eigendecomposition of the graph Laplacian matrix. We try to minimize the loss wrt the perturbed $G+\Delta{G}$ while making $\Delta{G}$ to be effective in terms of the Fisher information of the neural network. Our proposed model can consistently improve graph convolutional networks on semi-supervised node classification tasks with reasonable computational overhead. We present three different geometries on the manifold of graphs: the intrinsic geometry measures the information theoretic dynamics of a graph; the extrinsic geometry characterizes how such dynamics can affect externally a graph neural network; the embedding geometry is for measuring node embeddings. These new analytical tools are useful in developing a good understanding of graph neural networks and fostering new techniques.
To solve the problem that convolutional neural networks (CNNs) are difficult to process non-grid type relational data like graphs, Kipf et al. proposed a graph convolutional neural network (GCN). The core idea of the GCN is to perform two-fold informational fusion for each node in a given graph during each iteration: the fusion of graph structure information and the fusion of node feature dimensions. Because of the characteristic of the combinatorial generalizations, GCN has been widely used in the fields of scene semantic relationship analysis, natural language processing and few-shot learning etc. However, due to its two-fold informational fusion involves mathematical irreversible calculations, it is hard to explain the decision reason for the prediction of the each node classification. Unfortunately, most of the existing attribution analysis methods concentrate on the models like CNNs, which are utilized to process grid-like data. It is difficult to apply those analysis methods to the GCN directly. It is because compared with the independence among CNNs input data, there is correlation between the GCN input data. This resulting in the existing attribution analysis methods can only obtain the partial model contribution from the central node features to the final decision of the GCN, but ignores the other model contribution from central node features and its neighbor nodes features to that decision. To this end, we propose a gradient attribution analysis method for the GCN called Node Attribution Method (NAM), which can get the model contribution from not only the central node but also its neighbor nodes to the GCN output. We also propose the Node Importance Visualization (NIV) method to visualize the central node and its neighbor nodes based on the value of the contribution...
An implementation of "Binarized Attributed Network Embedding". Attributed network embedding enables joint representation learning of node links and attributes. Existing attributed network embedding models are designed in continuous Euclidean spaces which often introduce data redundancy and impose challenges to storage and computation costs. To this end, we present a Binarized Attributed Network Embedding model (BANE for short) to learn binary node representation. Specifically, we define a new Weisfeiler-Lehman proximity matrix to capture data dependence between node links and attributes by aggregating the information of node attributes and links from neighboring nodes to a given target node in a layer-wise manner. Based on the Weisfeiler-Lehman proximity matrix, we formulate a new Weisfiler-Lehman matrix factorization learning function under the binary node representation constraint. The learning problem is a mixed integer optimization and an efficient cyclic coordinate descent (CCD) algorithm is used as the solution. Node classification and link prediction experiments on real-world datasets show that the proposed BANE model outperforms the state-of-the-art network embedding methods.
Network embedding aims at learning the low-dimensional and continuous vector representation for each node in networks, which is useful in many real applications. While most existing network embedding methods only focus on the network structure, the rich text information associated with nodes, which is often closely related to network structure, is widely neglected. Thus, how to effectively incorporate text information into network embedding is a problem worth studying. To solve the problem, we propose a Text Enhanced Network Embedding (TENE) method under the framework of non-negative matrix factorization to integrate network structure and text information together. We explore the consistent relationship between node representations and text cluster structure to make the network embedding more informative and discriminative. TENE learns the representations of nodes under the guidance of both proximity matrix which captures the network structure and text cluster membership matrix derived from clustering for text information. We evaluate the quality of network embedding on the task of multi-class classification of nodes. Experimental results on all three real-world datasets show the superior performance of TENE compared with baselines.
We introduce PyTorch Geometric, a library for deep learning on irregularly structured input data such as graphs, point clouds and manifolds, built upon PyTorch. In addition to general graph data structures and processing methods, it contains a variety of recently published methods from the domains of relational learning and 3D data processing. PyTorch Geometric achieves high data throughput by leveraging sparse GPU acceleration, by providing dedicated CUDA kernels and by introducing efficient mini-batch handling for input examples of different size. In this work, we present the library in detail and perform a comprehensive comparative study of the implemented methods in homogeneous evaluation scenarios.
Graph processes model a number of important problems such as identifying the epicenter of an earthquake or predicting weather. In this paper, we propose a Graph Convolutional Recurrent Neural Network (GCRNN) architecture specifically tailored to deal with these problems. GCRNNs use convolutional filter banks to keep the number of trainable parameters independent of the size of the graph and of the time sequences considered. We also put forward Gated GCRNNs, a time-gated variation of GCRNNs akin to LSTMs. When compared with GNNs and another graph recurrent architecture in experiments using both synthetic and real-word data, GCRNNs significantly improve performance while using considerably less parameters.
Inferencing with network data necessitates the mapping of its nodes into a vector space, where the relationships are preserved. However, with multi-layered networks, where multiple types of relationships exist for the same set of nodes, it is crucial to exploit the information shared between layers, in addition to the distinct aspects of each layer. In this paper, we propose a novel approach that first obtains node embeddings in all layers jointly via DeepWalk on a \textit{supra} graph, which allows interactions between layers, and then fine-tunes the embeddings to encourage cohesive structure in the latent space. With empirical studies in node classification, link prediction and multi-layered community detection, we show that the proposed approach outperforms existing single- and multi-layered network embedding algorithms on several benchmarks. In addition to effectively scaling to a large number of layers (tested up to $37$), our approach consistently produces highly modular community structure, even when compared to methods that directly optimize for the modularity function.
Learning continuous representations of nodes is attracting growing interest in both academia and industry recently, due to their simplicity and effectiveness in a variety of applications. Most of existing node embedding algorithms and systems are capable of processing networks with hundreds of thousands or a few millions of nodes. However, how to scale them to networks that have tens of millions or even hundreds of millions of nodes remains a challenging problem. In this paper, we propose GraphVite, a high-performance CPU-GPU hybrid system for training node embeddings, by co-optimizing the algorithm and the system. On the CPU end, augmented edge samples are parallelly generated by random walks in an online fashion on the network, and serve as the training data. On the GPU end, a novel parallel negative sampling is proposed to leverage multiple GPUs to train node embeddings simultaneously, without much data transfer and synchronization. Moreover, an efficient collaboration strategy is proposed to further reduce the synchronization cost between CPUs and GPUs. Experiments on multiple real-world networks show that GraphVite is super efficient. It takes only about one minute for a network with 1 million nodes and 5 million edges on a single machine with 4 GPUs, and takes around 20 hours for a network with 66 million nodes and 1.8 billion edges. Compared to the current fastest system, GraphVite is about 50 times faster without any sacrifice on performance.