Instability of trained models, i.e., the dependence of individual node predictions on random factors, can affect reproducibility, reliability, and trust in machine learning systems. In this paper, we systematically assess the prediction instability of node classification with state-of-the-art Graph Neural Networks (GNNs). With our experiments, we establish that multiple instantiations of popular GNN models trained on the same data with the same model hyperparameters result in almost identical aggregated performance but display substantial disagreement in the predictions for individual nodes. We find that up to one third of the incorrectly classified nodes differ across algorithm runs. We identify correlations between hyperparameters, node properties, and the size of the training set with the stability of predictions. In general, maximizing model performance implicitly also reduces model instability.
The last years have witnessed the emergence of a promising self-supervised learning strategy, referred to as masked autoencoding. However, there is a lack of theoretical understanding of how masking matters on graph autoencoders (GAEs). In this work, we present masked graph autoencoder (MaskGAE), a self-supervised learning framework for graph-structured data. Different from standard GAEs, MaskGAE adopts masked graph modeling (MGM) as a principled pretext task - masking a portion of edges and attempting to reconstruct the missing part with partially visible, unmasked graph structure. To understand whether MGM can help GAEs learn better representations, we provide both theoretical and empirical evidence to comprehensively justify the benefits of this pretext task. Theoretically, we establish close connections between GAEs and contrastive learning, showing that MGM significantly improves the self-supervised learning scheme of GAEs. Empirically, we conduct extensive experiments on a variety of graph benchmarks, demonstrating the superiority of MaskGAE over several state-of-the-arts on both link prediction and node classification tasks.
Due to the superior performance of Graph Neural Networks (GNNs) in various domains, there is an increasing interest in the GNN explanation problem "\emph{which fraction of the input graph is the most crucial to decide the model's decision?}" Existing explanation methods focus on the supervised settings, \eg, node classification and graph classification, while the explanation for unsupervised graph-level representation learning is still unexplored. The opaqueness of the graph representations may lead to unexpected risks when deployed for high-stake decision-making scenarios. In this paper, we advance the Information Bottleneck principle (IB) to tackle the proposed explanation problem for unsupervised graph representations, which leads to a novel principle, \textit{Unsupervised Subgraph Information Bottleneck} (USIB). We also theoretically analyze the connection between graph representations and explanatory subgraphs on the label space, which reveals that the expressiveness and robustness of representations benefit the fidelity of explanatory subgraphs. Experimental results on both synthetic and real-world datasets demonstrate the superiority of our developed explainer and the validity of our theoretical analysis.
Graph Neural Networks (GNNs) have been predominant for graph learning tasks; however, recent studies showed that a well-known graph algorithm, Label Propagation (LP), combined with a shallow neural network can achieve comparable performance to GNNs in semi-supervised node classification on graphs with high homophily. In this paper, we show that this approach falls short on graphs with low homophily, where nodes often connect to the nodes of the opposite classes. To overcome this, we carefully design a combination of a base predictor with LP algorithm that enjoys a closed-form solution as well as convergence guarantees. Our algorithm first learns the class compatibility matrix and then aggregates label predictions using LP algorithm weighted by class compatibilities. On a wide variety of benchmarks, we show that our approach achieves the leading performance on graphs with various levels of homophily. Meanwhile, it has orders of magnitude fewer parameters and requires less execution time. Empirical evaluations demonstrate that simple adaptations of LP can be competitive in semi-supervised node classification in both homophily and heterophily regimes.
In this paper, we propose a simple yet effective graph neural network for directed graphs (digraph) based on the classic Singular Value Decomposition (SVD), named SVD-GCN. The new graph neural network is built upon the graph SVD-framelet to better decompose graph signals on the SVD ``frequency'' bands. Further the new framelet SVD-GCN is also scaled up for larger scale graphs via using Chebyshev polynomial approximation. Through empirical experiments conducted on several node classification datasets, we have found that SVD-GCN has remarkable improvements in a variety of graph node learning tasks and it outperforms GCN and many other state-of-the-art graph neural networks for digraphs. Moreover, we empirically demonstate that the SVD-GCN has great denoising capability and robustness to high level graph data attacks. The theoretical and experimental results prove that the SVD-GCN is effective on a variant of graph datasets, meanwhile maintaining stable and even better performance than the state-of-the-arts.
Classifying all cells in an organ is a relevant and difficult problem from plant developmental biology. We here abstract the problem into a new benchmark for node classification in a geo-referenced graph. Solving it requires learning the spatial layout of the organ including symmetries. To allow the convenient testing of new geometrical learning methods, the benchmark of Arabidopsis thaliana ovules is made available as a PyTorch data loader, along with a large number of precomputed features. Finally, we benchmark eight recent graph neural network architectures, finding that DeeperGCN currently works best on this problem.
We investigate graph neural networks on graphs with heterophily. Some existing methods amplify a node's neighborhood with multi-hop neighbors to include more nodes with homophily. However, it is a significant challenge to set personalized neighborhood sizes for different nodes. Further, for other homophilous nodes excluded in the neighborhood, they are ignored for information aggregation. To address these problems, we propose two models GloGNN and GloGNN++, which generate a node's embedding by aggregating information from global nodes in the graph. In each layer, both models learn a coefficient matrix to capture the correlations between nodes, based on which neighborhood aggregation is performed. The coefficient matrix allows signed values and is derived from an optimization problem that has a closed-form solution. We further accelerate neighborhood aggregation and derive a linear time complexity. We theoretically explain the models' effectiveness by proving that both the coefficient matrix and the generated node embedding matrix have the desired grouping effect. We conduct extensive experiments to compare our models against 11 other competitors on 15 benchmark datasets in a wide range of domains, scales and graph heterophilies. Experimental results show that our methods achieve superior performance and are also very efficient.
Nowadays, the analysis of complex phenomena modeled by graphs plays a crucial role in many real-world application domains where decisions can have a strong societal impact. However, numerous studies and papers have recently revealed that machine learning models could lead to potential disparate treatment between individuals and unfair outcomes. In that context, algorithmic contributions for graph mining are not spared by the problem of fairness and present some specific challenges related to the intrinsic nature of graphs: (1) graph data is non-IID, and this assumption may invalidate many existing studies in fair machine learning, (2) suited metric definitions to assess the different types of fairness with relational data and (3) algorithmic challenge on the difficulty of finding a good trade-off between model accuracy and fairness. This survey is the first one dedicated to fairness for relational data. It aims to present a comprehensive review of state-of-the-art techniques in fairness on graph mining and identify the open challenges and future trends. In particular, we start by presenting several sensible application domains and the associated graph mining tasks with a focus on edge prediction and node classification in the sequel. We also recall the different metrics proposed to evaluate potential bias at different levels of the graph mining process; then we provide a comprehensive overview of recent contributions in the domain of fair machine learning for graphs, that we classify into pre-processing, in-processing and post-processing models. We also propose to describe existing graph data, synthetic and real-world benchmarks. Finally, we present in detail five potential promising directions to advance research in studying algorithmic fairness on graphs.
Graph Convolutional Networks (GCNs) suffer from performance degradation when models go deeper. However, earlier works only attributed the performance degeneration to over-smoothing. In this paper, we conduct theoretical and experimental analysis to explore the fundamental causes of performance degradation in deep GCNs: over-smoothing and gradient vanishing have a mutually reinforcing effect that causes the performance to deteriorate more quickly in deep GCNs. On the other hand, existing anti-over-smoothing methods all perform full convolutions up to the model depth. They could not well resist the exponential convergence of over-smoothing due to model depth increasing. In this work, we propose a simple yet effective plug-and-play module, Skipnode, to overcome the performance degradation of deep GCNs. It samples graph nodes in each convolutional layer to skip the convolution operation. In this way, both over-smoothing and gradient vanishing can be effectively suppressed since (1) not all nodes'features propagate through full layers and, (2) the gradient can be directly passed back through ``skipped'' nodes. We provide both theoretical analysis and empirical evaluation to demonstrate the efficacy of Skipnode and its superiority over SOTA baselines.
Graph neural networks (GNNs) have achieved state-of-the-art performance in many graph-based tasks such as node classification and graph classification. However, many recent works have demonstrated that an attacker can mislead GNN models by slightly perturbing the graph structure. Existing attacks to GNNs are either under the less practical threat model where the attacker is assumed to access the GNN model parameters, or under the practical black-box threat model but consider perturbing node features that are shown to be not enough effective. In this paper, we aim to bridge this gap and consider black-box attacks to GNNs with structure perturbation as well as with theoretical guarantees. We propose to address this challenge through bandit techniques. Specifically, we formulate our attack as an online optimization with bandit feedback. This original problem is essentially NP-hard due to the fact that perturbing the graph structure is a binary optimization problem. We then propose an online attack based on bandit optimization which is proven to be {sublinear} to the query number $T$, i.e., $\mathcal{O}(\sqrt{N}T^{3/4})$ where $N$ is the number of nodes in the graph. Finally, we evaluate our proposed attack by conducting experiments over multiple datasets and GNN models. The experimental results on various citation graphs and image graphs show that our attack is both effective and efficient. Source code is available at~\url{https://github.com/Metaoblivion/Bandit_GNN_Attack}
Classification tasks on labeled graph-structured data have many important applications ranging from social recommendation to financial modeling. Deep neural networks are increasingly being used for node classification on graphs, wherein nodes with similar features have to be given the same label. Graph convolutional networks (GCNs) are one such widely studied neural network architecture that perform well on this task. However, powerful link-stealing attacks on GCNs have recently shown that even with black-box access to the trained model, inferring which links (or edges) are present in the training graph is practical. In this paper, we present a new neural network architecture called LPGNet for training on graphs with privacy-sensitive edges. LPGNet provides differential privacy (DP) guarantees for edges using a novel design for how graph edge structure is used during training. We empirically show that LPGNet models often lie in the sweet spot between providing privacy and utility: They can offer better utility than "trivially" private architectures which use no edge information (e.g., vanilla MLPs) and better resilience against existing link-stealing attacks than vanilla GCNs which use the full edge structure. LPGNet also offers consistently better privacy-utility tradeoffs than DPGCN, which is the state-of-the-art mechanism for retrofitting differential privacy into conventional GCNs, in most of our evaluated datasets.
Node classification on graphs can be formulated as the Dirichlet problem on graphs where the signal is given at the labeled nodes, and the harmonic extension is done on the unlabeled nodes. This paper considers a time-dependent version of the Dirichlet problem on graphs and shows how to improve its solution by learning the proper initialization vector on the unlabeled nodes. Further, we show that the improved solution is at par with state-of-the-art methods used for node classification. Finally, we conclude this paper by discussing the importance of parameter t, pros, and future directions.
Graph contrastive learning has gained significant progress recently. However, existing works have rarely explored non-aligned node-node contrasting. In this paper, we propose a novel graph contrastive learning method named RoSA that focuses on utilizing non-aligned augmented views for node-level representation learning. First, we leverage the earth mover's distance to model the minimum effort to transform the distribution of one view to the other as our contrastive objective, which does not require alignment between views. Then we introduce adversarial training as an auxiliary method to increase sampling diversity and enhance the robustness of our model. Experimental results show that RoSA outperforms a series of graph contrastive learning frameworks on homophilous, non-homophilous and dynamic graphs, which validates the effectiveness of our work. To the best of our awareness, RoSA is the first work focuses on the non-aligned node-node graph contrastive learning problem. Our codes are available at: \href{https://github.com/ZhuYun97/RoSA}{\texttt{https://github.com/ZhuYun97/RoSA}}
Given the ubiquitous existence of graph-structured data, learning the representations of nodes for the downstream tasks ranging from node classification, link prediction to graph classification is of crucial importance. Regarding missing link inference of diverse networks, we revisit the link prediction techniques and identify the importance of both the structural and attribute information. However, the available techniques either heavily count on the network topology which is spurious in practice or cannot integrate graph topology and features properly. To bridge the gap, we propose a bicomponent structural and attribute learning framework (BSAL) that is designed to adaptively leverage information from topology and feature spaces. Specifically, BSAL constructs a semantic topology via the node attributes and then gets the embeddings regarding the semantic view, which provides a flexible and easy-to-implement solution to adaptively incorporate the information carried by the node attributes. Then the semantic embedding together with topology embedding is fused together using an attention mechanism for the final prediction. Extensive experiments show the superior performance of our proposal and it significantly outperforms baselines on diverse research benchmarks.
This paper studies node classification in the inductive setting, i.e., aiming to learn a model on labeled training graphs and generalize it to infer node labels on unlabeled test graphs. This problem has been extensively studied with graph neural networks (GNNs) by learning effective node representations, as well as traditional structured prediction methods for modeling the structured output of node labels, e.g., conditional random fields (CRFs). In this paper, we present a new approach called the Structured Proxy Network (SPN), which combines the advantages of both worlds. SPN defines flexible potential functions of CRFs with GNNs. However, learning such a model is nontrivial as it involves optimizing a maximin game with high-cost inference. Inspired by the underlying connection between joint and marginal distributions defined by Markov networks, we propose to solve an approximate version of the optimization problem as a proxy, which yields a near-optimal solution, making learning more efficient. Extensive experiments on two settings show that our approach outperforms many competitive baselines.
Graph Neural Networks (GNNs) have been successfully used in many problems involving graph-structured data, achieving state-of-the-art performance. GNNs typically employ a message-passing scheme, in which every node aggregates information from its neighbors using a permutation-invariant aggregation function. Standard well-examined choices such as the mean or sum aggregation functions have limited capabilities, as they are not able to capture interactions among neighbors. In this work, we formalize these interactions using an information-theoretic framework that notably includes synergistic information. Driven by this definition, we introduce the Graph Ordering Attention (GOAT) layer, a novel GNN component that captures interactions between nodes in a neighborhood. This is achieved by learning local node orderings via an attention mechanism and processing the ordered representations using a recurrent neural network aggregator. This design allows us to make use of a permutation-sensitive aggregator while maintaining the permutation-equivariance of the proposed GOAT layer. The GOAT model demonstrates its increased performance in modeling graph metrics that capture complex information, such as the betweenness centrality and the effective size of a node. In practical use-cases, its superior modeling capability is confirmed through its success in several real-world node classification benchmarks.
Graph Representation Learning (GRL) has become central for characterizing structures of complex networks and performing tasks such as link prediction, node classification, network reconstruction, and community detection. Whereas numerous generative GRL models have been proposed, many approaches have prohibitive computational requirements hampering large-scale network analysis, fewer are able to explicitly account for structure emerging at multiple scales, and only a few explicitly respect important network properties such as homophily and transitivity. This paper proposes a novel scalable graph representation learning method named the Hierarchical Block Distance Model (HBDM). The HBDM imposes a multiscale block structure akin to stochastic block modeling (SBM) and accounts for homophily and transitivity by accurately approximating the latent distance model (LDM) throughout the inferred hierarchy. The HBDM naturally accommodates unipartite, directed, and bipartite networks whereas the hierarchy is designed to ensure linearithmic time and space complexity enabling the analysis of very large-scale networks. We evaluate the performance of the HBDM on massive networks consisting of millions of nodes. Importantly, we find that the proposed HBDM framework significantly outperforms recent scalable approaches in all considered downstream tasks. Surprisingly, we observe superior performance even imposing ultra-low two-dimensional embeddings facilitating accurate direct and hierarchical-aware network visualization and interpretation.
Graph neural networks (GNNs) are powerful tools for handling graph-structured data. However, their design often limits them to learning only higher-order feature interactions, leaving low-order feature interactions overlooked. To address this problem, we introduce a novel GNN method called explicit feature interaction-aware graph neural network (EFI-GNN). Unlike conventional GNNs, EFI-GNN is a multilayer linear network designed to model arbitrary-order feature interactions explicitly within graphs. To validate the efficacy of EFI-GNN, we conduct experiments using various datasets. The experimental results demonstrate that EFI-GNN has competitive performance with existing GNNs, and when a GNN is jointly trained with EFI-GNN, predictive performance sees an improvement. Furthermore, the predictions made by EFI-GNN are interpretable, owing to its linear construction. The source code of EFI-GNN is available at https://github.com/gim4855744/EFI-GNN
Graph structured data is ubiquitous in daily life and scientific areas and has attracted increasing attention. Graph Neural Networks (GNNs) have been proved to be effective in modeling graph structured data and many variants of GNN architectures have been proposed. However, much human effort is often needed to tune the architecture depending on different datasets. Researchers naturally adopt Automated Machine Learning on Graph Learning, aiming to reduce the human effort and achieve generally top-performing GNNs, but their methods focus more on the architecture search. To understand GNN practitioners' automated solutions, we organized AutoGraph Challenge at KDD Cup 2020, emphasizing on automated graph neural networks for node classification. We received top solutions especially from industrial tech companies like Meituan, Alibaba and Twitter, which are already open sourced on Github. After detailed comparisons with solutions from academia, we quantify the gaps between academia and industry on modeling scope, effectiveness and efficiency, and show that (1) academia AutoML for Graph solutions focus on GNN architecture search while industrial solutions, especially the winning ones in the KDD Cup, tend to obtain an overall solution (2) by neural architecture search only, academia solutions achieve on average 97.3% accuracy of industrial solutions (3) academia solutions are cheap to obtain with several GPU hours while industrial solutions take a few months' labors. Academic solutions also contain much fewer parameters.
Graph learning algorithms have attained state-of-the-art performance on many graph analysis tasks such as node classification, link prediction, and clustering. It has, however, become hard to track the field's burgeoning progress. One reason is due to the very small number of datasets used in practice to benchmark the performance of graph learning algorithms. This shockingly small sample size (~10) allows for only limited scientific insight into the problem. In this work, we aim to address this deficiency. We propose to generate synthetic graphs, and study the behaviour of graph learning algorithms in a controlled scenario. We develop a fully-featured synthetic graph generator that allows deep inspection of different models. We argue that synthetic graph generations allows for thorough investigation of algorithms and provides more insights than overfitting on three citation datasets. In the case study, we show how our framework provides insight into unsupervised and supervised graph neural network models.