While graph neural networks (GNNs) have been shown to perform well on graph-based data from a variety of fields, they suffer from a lack of transparency and accountability, which hinders trust and consequently the deployment of such models in high-stake and safety-critical scenarios. Even though recent research has investigated methods for explaining GNNs, these methods are limited to single-instance explanations, also known as local explanations. Motivated by the aim of providing global explanations, we adapt the well-known Automated Concept-based Explanation approach (Ghorbani et al., 2019) to GNN node and graph classification, and propose GCExplainer. GCExplainer is an unsupervised approach for post-hoc discovery and extraction of global concept-based explanations for GNNs, which puts the human in the loop. We demonstrate the success of our technique on five node classification datasets and two graph classification datasets, showing that we are able to discover and extract high-quality concept representations by putting the human in the loop. We achieve a maximum completeness score of 1 and an average completeness score of 0.753 across the datasets. Finally, we show that the concept-based explanations provide an improved insight into the datasets and GNN models compared to the state-of-the-art explanations produced by GNNExplainer (Ying et al., 2019).
Graph neural networks (GNNs) have been widely used in many graph-based tasks such as node classification, link prediction, and node clustering. However, GNNs gain their performance benefits mainly from performing the feature propagation and smoothing across the edges of the graph, thus requiring sufficient connectivity and label information for effective propagation. Unfortunately, many real-world networks are sparse in terms of both edges and labels, leading to sub-optimal performance of GNNs. Recent interest in this sparse problem has focused on the self-training approach, which expands supervised signals with pseudo labels. Nevertheless, the self-training approach inherently cannot realize the full potential of refining the learning performance on sparse graphs due to the unsatisfactory quality and quantity of pseudo labels. In this paper, we propose ROD, a novel reception-aware online knowledge distillation approach for sparse graph learning. We design three supervision signals for ROD: multi-scale reception-aware graph knowledge, task-based supervision, and rich distilled knowledge, allowing online knowledge transfer in a peer-teaching manner. To extract knowledge concealed in the multi-scale reception fields, ROD explicitly requires individual student models to preserve different levels of locality information. For a given task, each student would predict based on its reception-scale knowledge, while simultaneously a strong teacher is established on-the-fly by combining multi-scale knowledge. Our approach has been extensively evaluated on 9 datasets and a variety of graph-based tasks, including node classification, link prediction, and node clustering. The result demonstrates that ROD achieves state-of-art performance and is more robust for the graph sparsity.
Graph neural networks (GNNs) have achieved remarkable success as a framework for deep learning on graph-structured data. However, GNNs are fundamentally limited by their tree-structured inductive bias: the WL-subtree kernel formulation bounds the representational capacity of GNNs, and polynomial-time GNNs are provably incapable of recognizing triangles in a graph. In this work, we propose to augment the GNN message-passing operations with information defined on ego graphs (i.e., the induced subgraph surrounding each node). We term these approaches Ego-GNNs and show that Ego-GNNs are provably more powerful than standard message-passing GNNs. In particular, we show that Ego-GNNs are capable of recognizing closed triangles, which is essential given the prominence of transitivity in real-world graphs. We also motivate our approach from the perspective of graph signal processing as a form of multiplex graph convolution. Experimental results on node classification using synthetic and real data highlight the achievable performance gains using this approach.
In this paper, we describe a reproduction of the Relational Graph Convolutional Network (RGCN). Using our reproduction, we explain the intuition behind the model. Our reproduction results empirically validate the correctness of our implementations using benchmark Knowledge Graph datasets on node classification and link prediction tasks. Our explanation provides a friendly understanding of the different components of the RGCN for both users and researchers extending the RGCN approach. Furthermore, we introduce two new configurations of the RGCN that are more parameter efficient. The code and datasets are available at https://github.com/thiviyanT/torch-rgcn.
Recently, Network Embedding (NE) has become one of the most attractive research topics in machine learning and data mining. NE approaches have achieved promising performance in various of graph mining tasks including link prediction and node clustering and classification. A wide variety of NE methods focus on the proximity of networks. They learn community-oriented embedding for each node, where the corresponding representations are similar if two nodes are closer to each other in the network. Meanwhile, there is another type of structural similarity, i.e., role-based similarity, which is usually complementary and completely different from the proximity. In order to preserve the role-based structural similarity, the problem of role-oriented NE is raised. However, compared to community-oriented NE problem, there are only a few role-oriented embedding approaches proposed recently. Although less explored, considering the importance of roles in analyzing networks and many applications that role-oriented NE can shed light on, it is necessary and timely to provide a comprehensive overview of existing role-oriented NE methods. In this review, we first clarify the differences between community-oriented and role-oriented network embedding. Afterwards, we propose a general framework for understanding role-oriented NE and a two-level categorization to better classify existing methods. Then, we select some representative methods according to the proposed categorization and briefly introduce them by discussing their motivation, development and differences. Moreover, we conduct comprehensive experiments to empirically evaluate these methods on a variety of role-related tasks including node classification and clustering (role discovery), top-k similarity search and visualization using some widely used synthetic and real-world datasets...
Biological spiking neurons with intrinsic dynamics underlie the powerful representation and learning capabilities of the brain for processing multimodal information in complex environments. Despite recent tremendous progress in spiking neural networks (SNNs) for handling Euclidean-space tasks, it still remains challenging to exploit SNNs in processing non-Euclidean-space data represented by graph data, mainly due to the lack of effective modeling framework and useful training techniques. Here we present a general spike-based modeling framework that enables the direct training of SNNs for graph learning. Through spatial-temporal unfolding for spiking data flows of node features, we incorporate graph convolution filters into spiking dynamics and formalize a synergistic learning paradigm. Considering the unique features of spike representation and spiking dynamics, we propose a spatial-temporal feature normalization (STFN) technique suitable for SNN to accelerate convergence. We instantiate our methods into two spiking graph models, including graph convolution SNNs and graph attention SNNs, and validate their performance on three node-classification benchmarks, including Cora, Citeseer, and Pubmed. Our model can achieve comparable performance with the state-of-the-art graph neural network (GNN) models with much lower computation costs, demonstrating great benefits for the execution on neuromorphic hardware and prompting neuromorphic applications in graphical scenarios.
The Graph Convolutional Networks (GCN) proposed by Kipf and Welling is an effective model for semi-supervised learning, but faces the obstacle of over-smoothing, which will weaken the representation ability of GCN. Recently some works are proposed to tackle above limitation by randomly perturbing graph topology or feature matrix to generate data augmentations as input for training. However, these operations inevitably do damage to the integrity of information structures and have to sacrifice the smoothness of feature manifold. In this paper, we first introduce a novel graph entropy definition as a measure to quantitatively evaluate the smoothness of a data manifold and then point out that this graph entropy is controlled by triangle motif-based information structures. Considering the preservation of graph entropy, we propose an effective strategy to generate randomly perturbed training data but maintain both graph topology and graph entropy. Extensive experiments have been conducted on real-world datasets and the results verify the effectiveness of our proposed method in improving semi-supervised node classification accuracy compared with a surge of baselines. Beyond that, our proposed approach could significantly enhance the robustness of training process for GCN.
Owing to the remarkable capability of extracting effective graph embeddings, graph convolutional network (GCN) and its variants have been successfully applied to a broad range of tasks, such as node classification, link prediction, and graph classification. Traditional GCN models suffer from the issues of overfitting and oversmoothing, while some recent techniques like DropEdge could alleviate these issues and thus enable the development of deep GCN. However, training GCN models is non-trivial, as it is sensitive to the choice of hyperparameters such as dropout rate and learning weight decay, especially for deep GCN models. In this paper, we aim to automate the training of GCN models through hyperparameter optimization. To be specific, we propose a self-tuning GCN approach with an alternate training algorithm, and further extend our approach by incorporating the population based training scheme. Experimental results on three benchmark datasets demonstrate the effectiveness of our approaches on optimizing multi-layer GCN, compared with several representative baselines.
Network data are ubiquitous in modern machine learning, with tasks of interest including node classification, node clustering and link prediction. A frequent approach begins by learning an Euclidean embedding of the network, to which algorithms developed for vector-valued data are applied. For large networks, embeddings are learned using stochastic gradient methods where the sub-sampling scheme can be freely chosen. Despite the strong empirical performance of such methods, they are not well understood theoretically. Our work encapsulates representation methods using a subsampling approach, such as node2vec, into a single unifying framework. We prove, under the assumption that the graph is exchangeable, that the distribution of the learned embedding vectors asymptotically decouples. Moreover, we characterize the asymptotic distribution and provided rates of convergence, in terms of the latent parameters, which includes the choice of loss function and the embedding dimension. This provides a theoretical foundation to understand what the embedding vectors represent and how well these methods perform on downstream tasks. Notably, we observe that typically used loss functions may lead to shortcomings, such as a lack of Fisher consistency.
Learning with graphs has attracted significant attention recently. Existing representation learning methods on graphs have achieved state-of-the-art performance on various graph-related tasks such as node classification, link prediction, etc. However, we observe that these methods could leak serious private information. For instance, one can accurately infer the links (or node identity) in a graph from a node classifier (or link predictor) trained on the learnt node representations by existing methods. To address the issue, we propose a privacy-preserving representation learning framework on graphs from the \emph{mutual information} perspective. Specifically, our framework includes a primary learning task and a privacy protection task, and we consider node classification and link prediction as the two tasks of interest. Our goal is to learn node representations such that they can be used to achieve high performance for the primary learning task, while obtaining performance for the privacy protection task close to random guessing. We formally formulate our goal via mutual information objectives. However, it is intractable to compute mutual information in practice. Then, we derive tractable variational bounds for the mutual information terms, where each bound can be parameterized via a neural network. Next, we train these parameterized neural networks to approximate the true mutual information and learn privacy-preserving node representations. We finally evaluate our framework on various graph datasets.
In the big data era, the relationship between entries becomes more and more complex. Many graph (or network) algorithms have already paid attention to dynamic networks, which are more suitable than static ones for fitting the complex real-world scenarios with evolving structures and features. To contribute to the dynamic network representation learning and mining research, we provide a new bunch of label-adequate, dynamics-meaningful, and attribute-sufficient dynamic networks from the health domain. To be specific, in our proposed repository DPPIN, we totally have 12 individual dynamic network datasets at different scales, and each dataset is a dynamic protein-protein interaction network describing protein-level interactions of yeast cells. We hope these domain-specific node features, structure evolution patterns, and node and graph labels could inspire the regularization techniques to increase the performance of graph machine learning algorithms in a more complex setting. Also, we link potential applications with our DPPIN by designing various dynamic graph experiments, where DPPIN could indicate future research opportunities for some tasks by presenting challenges on state-of-the-art baseline algorithms. Finally, we identify future directions to improve the utility of this repository and welcome constructive inputs from the community. All resources (e.g., data and code) of this work are deployed and publicly available at https://github.com/DongqiFu/DPPIN.
Graph neural networks (GNNs) have been widely used in various graph-related problems such as node classification and graph classification, where superior performance is mainly established when natural node features are available. However, it is not well understood how GNNs work without natural node features, especially regarding the various ways to construct artificial ones. In this paper, we point out the two types of artificial node features, i.e., positional and structural node features, and provide insights on why each of them is more appropriate for certain tasks, i.e., positional node classification, structural node classification, and graph classification. Extensive experimental results on 10 benchmark datasets validate our insights, thus leading to a practical guideline on the choices between different artificial node features for GNNs on non-attributed graphs. The code is available at https://github.com/zjzijielu/gnn-positional-structural-node-features.
Graph convolution networks (GCN), which recently becomes new state-of-the-art method for graph node classification, recommendation and other applications, has not been successfully applied to industrial-scale search engine yet. In this proposal, we introduce our approach, namely SearchGCN, for embedding-based candidate retrieval in one of the largest e-commerce search engine in the world. Empirical studies demonstrate that SearchGCN learns better embedding representations than existing methods, especially for long tail queries and items. Thus, SearchGCN has been deployed into JD.com's search production since July 2020.
Graph neural networks (GNNs) have achieved great success in many graph-based tasks. Much work is dedicated to empowering GNNs with the adaptive locality ability, which enables measuring the importance of neighboring nodes to the target node by a node-specific mechanism. However, the current node-specific mechanisms are deficient in distinguishing the importance of nodes in the topology structure. We believe that the structural importance of neighboring nodes is closely related to their importance in aggregation. In this paper, we introduce discrete graph curvature (the Ricci curvature) to quantify the strength of structural connection of pairwise nodes. And we propose Curvature Graph Neural Network (CGNN), which effectively improves the adaptive locality ability of GNNs by leveraging the structural property of graph curvature. To improve the adaptability of curvature to various datasets, we explicitly transform curvature into the weights of neighboring nodes by the necessary Negative Curvature Processing Module and Curvature Normalization Module. Then, we conduct numerous experiments on various synthetic datasets and real-world datasets. The experimental results on synthetic datasets show that CGNN effectively exploits the topology structure information, and the performance is improved significantly. CGNN outperforms the baselines on 5 dense node classification benchmark datasets. This study deepens the understanding of how to utilize advanced topology information and assign the importance of neighboring nodes from the perspective of graph curvature and encourages us to bridge the gap between graph theory and neural networks.
Graph Neural Networks (GNNs) require a relatively large number of labeled nodes and a reliable/uncorrupted graph connectivity structure in order to obtain good performance on the semi-supervised node classification task. The performance of GNNs can degrade significantly as the number of labeled nodes decreases or the graph connectivity structure is corrupted by adversarial attacks or due to noises in data measurement /collection. Therefore, it is important to develop GNN models that are able to achieve good performance when there is limited supervision knowledge -- a few labeled nodes and noisy graph structures. In this paper, we propose a novel Dual GNN learning framework to address this challenge task. The proposed framework has two GNN based node prediction modules. The primary module uses the input graph structure to induce regular node embeddings and predictions with a regular GNN baseline, while the auxiliary module constructs a new graph structure through fine-grained spectral clusterings and learns new node embeddings and predictions. By integrating the two modules in a dual GNN learning framework, we perform joint learning in an end-to-end fashion. This general framework can be applied on many GNN baseline models. The experimental results validate that the proposed dual GNN framework can greatly outperform the GNN baseline methods when the labeled nodes are scarce and the graph connectivity structure is noisy.
Hypergraphs are used to model higher-order interactions amongst agents and there exist many practically relevant instances of hypergraph datasets. To enable efficient processing of hypergraph-structured data, several hypergraph neural network platforms have been proposed for learning hypergraph properties and structure, with a special focus on node classification. However, almost all existing methods use heuristic propagation rules and offer suboptimal performance on many datasets. We propose AllSet, a new hypergraph neural network paradigm that represents a highly general framework for (hyper)graph neural networks and for the first time implements hypergraph neural network layers as compositions of two multiset functions that can be efficiently learned for each task and each dataset. Furthermore, AllSet draws on new connections between hypergraph neural networks and recent advances in deep learning of multiset functions. In particular, the proposed architecture utilizes Deep Sets and Set Transformer architectures that allow for significant modeling flexibility and offer high expressive power. To evaluate the performance of AllSet, we conduct the most extensive experiments to date involving ten known benchmarking datasets and three newly curated datasets that represent significant challenges for hypergraph node classification. The results demonstrate that AllSet has the unique ability to consistently either match or outperform all other hypergraph neural networks across the tested datasets.
Graph Neural Networks (GNNs) have shown excellent performance on graphs that exhibit strong homophily with respect to the node labels i.e. connected nodes have same labels. However, they perform poorly on heterophilic graphs. Recent approaches have typically modified aggregation schemes, designed adaptive graph filters, etc. to address this limitation. In spite of this, the performance on heterophilic graphs can still be poor. We propose a simple alternative method that exploits Truncated Singular Value Decomposition (TSVD) of topological structure and node features. Our approach achieves up to ~30% improvement in performance over state-of-the-art methods on heterophilic graphs. This work is an early investigation into methods that differ from aggregation based approaches. Our experimental results suggest that it might be important to explore other alternatives to aggregation methods for heterophilic setting.
Structural features are important features in a geometrical graph. Although there are some correlation analysis of features based on covariance, there is no relevant research on structural feature correlation analysis with graph neural networks. In this paper, we introuduce graph feature to feature (Fea2Fea) prediction pipelines in a low dimensional space to explore some preliminary results on structural feature correlation, which is based on graph neural network. The results show that there exists high correlation between some of the structural features. An irredundant feature combination with initial node features, which is filtered by graph neural network has improved its classification accuracy in some graph-based tasks. We compare differences between concatenation methods on connecting embeddings between features and show that the simplest is the best. We generalize on the synthetic geometric graphs and certify the results on prediction difficulty between structural features.
Conventional representation learning algorithms for knowledge graphs (KG) map each entity to a unique embedding vector. Such a shallow lookup results in a linear growth of memory consumption for storing the embedding matrix and incurs high computational costs when working with real-world KGs. Drawing parallels with subword tokenization commonly used in NLP, we explore the landscape of more parameter-efficient node embedding strategies with possibly sublinear memory requirements. To this end, we propose NodePiece, an anchor-based approach to learn a fixed-size entity vocabulary. In NodePiece, a vocabulary of subword/sub-entity units is constructed from anchor nodes in a graph with known relation types. Given such a fixed-size vocabulary, it is possible to bootstrap an encoding and embedding for any entity, including those unseen during training. Experiments show that NodePiece performs competitively in node classification, link prediction, and relation prediction tasks while retaining less than 10% of explicit nodes in a graph as anchors and often having 10x fewer parameters. To this end, we show that a NodePiece-enabled model outperforms existing shallow models on a large OGB WikiKG 2 graph having 70x fewer parameters.
Recently, Graph Neural Network (GNN) has achieved remarkable success in various real-world problems on graph data. However in most industries, data exists in the form of isolated islands and the data privacy and security is also an important issue. In this paper, we propose FedVGCN, a federated GCN learning paradigm for privacy-preserving node classification task under data vertically partitioned setting, which can be generalized to existing GCN models. Specifically, we split the computation graph data into two parts. For each iteration of the training process, the two parties transfer intermediate results to each other under homomorphic encryption. We conduct experiments on benchmark data and the results demonstrate the effectiveness of FedVGCN in the case of GraphSage.