Recently, Transformers for graph representation learning have become increasingly popular, achieving state-of-the-art performance on a wide-variety of graph datasets, either alone or in combination with message-passing graph neural networks (MP-GNNs). Infusing graph inductive-biases in the innately structure-agnostic transformer architecture in the form of structural or positional encodings (PEs) is key to achieving these impressive results. However, designing such encodings is tricky and disparate attempts have been made to engineer such encodings including Laplacian eigenvectors, relative random-walk probabilities (RRWP), spatial encodings, centrality encodings, edge encodings etc. In this work, we argue that such encodings may not be required at all, provided the attention mechanism itself incorporates information about the graph structure. We introduce Eigenformer, a Graph Transformer employing a novel spectrum-aware attention mechanism cognizant of the Laplacian spectrum of the graph, and empirically show that it achieves performance competetive with SOTA Graph Transformers on a number of standard GNN benchmarks. Additionally, we theoretically prove that Eigenformer can express various graph structural connectivity matrices, which is particularly essential when learning over smaller graphs.
This paper studies structured node classification on graphs, where the predictions should consider dependencies between the node labels. In particular, we focus on solving the problem for partially labeled graphs where it is essential to incorporate the information in the known label for predicting the unknown labels. To address this issue, we propose a novel framework leveraging the diffusion probabilistic model for structured node classification (DPM-SNC). At the heart of our framework is the extraordinary capability of DPM-SNC to (a) learn a joint distribution over the labels with an expressive reverse diffusion process and (b) make predictions conditioned on the known labels utilizing manifold-constrained sampling. Since the DPMs lack training algorithms for partially labeled data, we design a novel training algorithm to apply DPMs, maximizing a new variational lower bound. We also theoretically analyze how DPMs benefit node classification by enhancing the expressive power of GNNs based on proposing AGG-WL, which is strictly more powerful than the classic 1-WL test. We extensively verify the superiority of our DPM-SNC in diverse scenarios, which include not only the transductive setting on partially labeled graphs but also the inductive setting and unlabeled graphs.
GNNs are widely used to solve various tasks including node classification and link prediction. Most of the GNN architectures assume the initial embedding to be random or generated from popular distributions. These initial embeddings require multiple layers of transformation to converge into a meaningful latent representation. While number of layers allow accumulation of larger neighbourhood of a node it also introduce the problem of over-smoothing. In addition, GNNs are inept at representing structural information. For example, the output embedding of a node does not capture its triangles participation. In this paper, we presented a novel feature extraction methodology GraphViz2Vec that can capture the structural information of a node's local neighbourhood to create meaningful initial embeddings for a GNN model. These initial embeddings helps existing models achieve state-of-the-art results in various classification tasks. Further, these initial embeddings help the model to produce desired results with only two layers which in turn reduce the problem of over-smoothing. The initial encoding of a node is obtained from an image classification model trained on multiple energy diagrams of its local neighbourhood. These energy diagrams are generated with the induced sub-graph of the nodes traversed by multiple random walks. The generated encodings increase the performance of existing models on classification tasks (with a mean increase of $4.65\%$ and $2.58\%$ for the node and link classification tasks, respectively), with some models achieving state-of-the-art results.
Graph neural networks (GNNs) demonstrate a robust capability for representation learning on graphs with complex structures, showcasing superior performance in various applications. The majority of existing GNNs employ a graph convolution operation by using both attribute and structure information through coupled learning. In essence, GNNs, from an optimization perspective, seek to learn a consensus and compromise embedding representation that balances attribute and graph information, selectively exploring and retaining valid information. To obtain a more comprehensive embedding representation of nodes, a novel GNNs framework, dubbed Decoupled Graph Neural Networks (DGNN), is introduced. DGNN explores distinctive embedding representations from the attribute and graph spaces by decoupled terms. Considering that semantic graph, constructed from attribute feature space, consists of different node connection information and provides enhancement for the topological graph, both topological and semantic graphs are combined for the embedding representation learning. Further, structural consistency among attribute embedding and graph embeddings is promoted to effectively remove redundant information and establish soft connection. This involves promoting factor sharing for adjacency reconstruction matrices, facilitating the exploration of a consensus and high-level correlation. Finally, a more powerful and complete representation is achieved through the concatenation of these embeddings. Experimental results conducted on several graph benchmark datasets verify its superiority in node classification task.
Graphs are widely used to model relational data. As graphs are getting larger and larger in real-world scenarios, there is a trend to store and compute subgraphs in multiple local systems. For example, recently proposed \emph{subgraph federated learning} methods train Graph Neural Networks (GNNs) distributively on local subgraphs and aggregate GNN parameters with a central server. However, existing methods have the following limitations: (1) The links between local subgraphs are missing in subgraph federated learning. This could severely damage the performance of GNNs that follow message-passing paradigms to update node/edge features. (2) Most existing methods overlook the subgraph heterogeneity issue, brought by subgraphs being from different parts of the whole graph. To address the aforementioned challenges, we propose a scalable \textbf{Fed}erated \textbf{G}raph \textbf{T}ransformer (\textbf{FedGT}) in the paper. Firstly, we design a hybrid attention scheme to reduce the complexity of the Graph Transformer to linear while ensuring a global receptive field with theoretical bounds. Specifically, each node attends to the sampled local neighbors and a set of curated global nodes to learn both local and global information and be robust to missing links. The global nodes are dynamically updated during training with an online clustering algorithm to capture the data distribution of the corresponding local subgraph. Secondly, FedGT computes clients' similarity based on the aligned global nodes with optimal transport. The similarity is then used to perform weighted averaging for personalized aggregation, which well addresses the data heterogeneity problem. Moreover, local differential privacy is applied to further protect the privacy of clients. Finally, extensive experimental results on 6 datasets and 2 subgraph settings demonstrate the superiority of FedGT.
In recent years, spectral graph neural networks, characterized by polynomial filters, have garnered increasing attention and have achieved remarkable performance in tasks such as node classification. These models typically assume that eigenvalues for the normalized Laplacian matrix are distinct from each other, thus expecting a polynomial filter to have a high fitting ability. However, this paper empirically observes that normalized Laplacian matrices frequently possess repeated eigenvalues. Moreover, we theoretically establish that the number of distinguishable eigenvalues plays a pivotal role in determining the expressive power of spectral graph neural networks. In light of this observation, we propose an eigenvalue correction strategy that can free polynomial filters from the constraints of repeated eigenvalue inputs. Concretely, the proposed eigenvalue correction strategy enhances the uniform distribution of eigenvalues, thus mitigating repeated eigenvalues, and improving the fitting capacity and expressive power of polynomial filters. Extensive experimental results on both synthetic and real-world datasets demonstrate the superiority of our method. The code is available at: https://github.com/Lukangkang123/EC-GNN
The vanilla Graph Convolutional Network (GCN) uses a low-pass filter to extract low-frequency signals from graph topology, which may lead to the over-smoothing problem when GCN goes deep. To this end, various methods have been proposed to create an adaptive filter by incorporating an extra filter (e.g., a high-pass filter) extracted from the graph topology. However, these methods heavily rely on topological information and ignore the node attribute space, which severely sacrifices the expressive power of the deep GCNs, especially when dealing with disassortative graphs. In this paper, we propose a cross-space adaptive filter, called CSF, to produce the adaptive-frequency information extracted from both the topology and attribute spaces. Specifically, we first derive a tailored attribute-based high-pass filter that can be interpreted theoretically as a minimizer for semi-supervised kernel ridge regression. Then, we cast the topology-based low-pass filter as a Mercer's kernel within the context of GCNs. This serves as a foundation for combining it with the attribute-based filter to capture the adaptive-frequency information. Finally, we derive the cross-space filter via an effective multiple-kernel learning strategy, which unifies the attribute-based high-pass filter and the topology-based low-pass filter. This helps to address the over-smoothing problem while maintaining effectiveness. Extensive experiments demonstrate that CSF not only successfully alleviates the over-smoothing problem but also promotes the effectiveness of the node classification task.
In the web era, graph machine learning has been widely used on ubiquitous graph-structured data. As a pivotal component for bolstering web security and enhancing the robustness of graph-based applications, the significance of graph anomaly detection is continually increasing. While Graph Neural Networks (GNNs) have demonstrated efficacy in supervised and semi-supervised graph anomaly detection, their performance is contingent upon the availability of sufficient ground truth labels. The labor-intensive nature of identifying anomalies from complex graph structures poses a significant challenge in real-world applications. Despite that, the indirect supervision signals from other tasks (e.g., node classification) are relatively abundant. In this paper, we propose a novel MultItask acTIve Graph Anomaly deTEction framework, namely MITIGATE. Firstly, by coupling node classification tasks, MITIGATE obtains the capability to detect out-of-distribution nodes without known anomalies. Secondly, MITIGATE quantifies the informativeness of nodes by the confidence difference across tasks, allowing samples with conflicting predictions to provide informative yet not excessively challenging information for subsequent training. Finally, to enhance the likelihood of selecting representative nodes that are distant from known patterns, MITIGATE adopts a masked aggregation mechanism for distance measurement, considering both inherent features of nodes and current labeled status. Empirical studies on four datasets demonstrate that MITIGATE significantly outperforms the state-of-the-art methods for anomaly detection. Our code is publicly available at: https://github.com/AhaChang/MITIGATE.
Despite remarkable success in diverse web-based applications, Graph Neural Networks(GNNs) inherit and further exacerbate historical discrimination and social stereotypes, which critically hinder their deployments in high-stake domains such as online clinical diagnosis, financial crediting, etc. However, current fairness research that primarily craft on i.i.d data, cannot be trivially replicated to non-i.i.d. graph structures with topological dependence among samples. Existing fair graph learning typically favors pairwise constraints to achieve fairness but fails to cast off dimensional limitations and generalize them into multiple sensitive attributes; besides, most studies focus on in-processing techniques to enforce and calibrate fairness, constructing a model-agnostic debiasing GNN framework at the pre-processing stage to prevent downstream misuses and improve training reliability is still largely under-explored. Furthermore, previous work on GNNs tend to enhance either fairness or privacy individually but few probe into their interplays. In this paper, we propose a novel model-agnostic debiasing framework named MAPPING (\underline{M}asking \underline{A}nd \underline{P}runing and Message-\underline{P}assing train\underline{ING}) for fair node classification, in which we adopt the distance covariance($dCov$)-based fairness constraints to simultaneously reduce feature and topology biases in arbitrary dimensions, and combine them with adversarial debiasing to confine the risks of attribute inference attacks. Experiments on real-world datasets with different GNN variants demonstrate the effectiveness and flexibility of MAPPING. Our results show that MAPPING can achieve better trade-offs between utility and fairness, and mitigate privacy risks of sensitive information leakage.
Graph Neural Networks (GNNs) have shown great power for learning and mining on graphs, and Graph Structure Learning (GSL) plays an important role in boosting GNNs with a refined graph. In the literature, most GSL solutions either primarily focus on structure refinement with task-specific supervision (i.e., node classification), or overlook the inherent weakness of GNNs themselves (e.g., over-squashing), resulting in suboptimal performance despite sophisticated designs. In light of these limitations, we propose to study self-supervised graph structure-feature co-refinement for effectively alleviating the issue of over-squashing in typical GNNs. In this paper, we take a fundamentally different perspective of the Ricci curvature in Riemannian geometry, in which we encounter the challenges of modeling, utilizing and computing Ricci curvature. To tackle these challenges, we present a self-supervised Riemannian model, DeepRicci. Specifically, we introduce a latent Riemannian space of heterogeneous curvatures to model various Ricci curvatures, and propose a gyrovector feature mapping to utilize Ricci curvature for typical GNNs. Thereafter, we refine node features by geometric contrastive learning among different geometric views, and simultaneously refine graph structure by backward Ricci flow based on a novel formulation of differentiable Ricci curvature. Finally, extensive experiments on public datasets show the superiority of DeepRicci, and the connection between backward Ricci flow and over-squashing. Codes of our work are given in https://github.com/RiemanGraph/.
Graph contrastive learning (GCL), learning the node representation by contrasting two augmented graphs in a self-supervised way, has attracted considerable attention. GCL is usually believed to learn the invariant representation. However, does this understanding always hold in practice? In this paper, we first study GCL from the perspective of causality. By analyzing GCL with the structural causal model (SCM), we discover that traditional GCL may not well learn the invariant representations due to the non-causal information contained in the graph. How can we fix it and encourage the current GCL to learn better invariant representations? The SCM offers two requirements and motives us to propose a novel GCL method. Particularly, we introduce the spectral graph augmentation to simulate the intervention upon non-causal factors. Then we design the invariance objective and independence objective to better capture the causal factors. Specifically, (i) the invariance objective encourages the encoder to capture the invariant information contained in causal variables, and (ii) the independence objective aims to reduce the influence of confounders on the causal variables. Experimental results demonstrate the effectiveness of our approach on node classification tasks.
Graph condensation has emerged as an intriguing technique to save the expensive training costs of Graph Neural Networks (GNNs) by substituting a condensed small graph with the original graph. Despite the promising results achieved, previous methods usually employ an entangled paradigm of redundant parameters (nodes, edges, GNNs), which incurs complex joint optimization during condensation. This paradigm has considerably impeded the scalability of graph condensation, making it challenging to condense extremely large-scale graphs and generate high-fidelity condensed graphs. Therefore, we propose to disentangle the condensation process into a two-stage GNN-free paradigm, independently condensing nodes and generating edges while eliminating the need to optimize GNNs at the same time. The node condensation module avoids the complexity of GNNs by focusing on node feature alignment with anchors of the original graph, while the edge translation module constructs the edges of the condensed nodes by transferring the original structure knowledge with neighborhood anchors. This simple yet effective approach achieves at least 10 times faster than state-of-the-art methods with comparable accuracy on medium-scale graphs. Moreover, the proposed DisCo can successfully scale up to the Ogbn-papers100M graph containing over 100 million nodes with flexible reduction rates and improves performance on the second-largest Ogbn-products dataset by over 5%. Extensive downstream tasks and ablation study on five common datasets further demonstrate the effectiveness of the proposed DisCo framework. Our code is available at https://github.com/BangHonor/DisCo.
Recently, Federated Graph Learning (FGL) has attracted significant attention as a distributed framework based on graph neural networks, primarily due to its capability to break data silos. Existing FGL studies employ community split on the homophilous global graph by default to simulate federated semi-supervised node classification settings. Such a strategy assumes the consistency of topology between the multi-client subgraphs and the global graph, where connected nodes are highly likely to possess similar feature distributions and the same label. However, in real-world implementations, the varying perspectives of local data engineering result in various subgraph topologies, posing unique heterogeneity challenges in FGL. Unlike the well-known label Non-independent identical distribution (Non-iid) problems in federated learning, FGL heterogeneity essentially reveals the topological divergence among multiple clients, namely homophily or heterophily. To simulate and handle this unique challenge, we introduce the concept of structure Non-iid split and then present a new paradigm called \underline{Ada}ptive \underline{F}ederated \underline{G}raph \underline{L}earning (AdaFGL), a decoupled two-step personalized approach. To begin with, AdaFGL employs standard multi-client federated collaborative training to acquire the federated knowledge extractor by aggregating uploaded models in the final round at the server. Then, each client conducts personalized training based on the local subgraph and the federated knowledge extractor. Extensive experiments on the 12 graph benchmark datasets validate the superior performance of AdaFGL over state-of-the-art baselines. Specifically, in terms of test accuracy, our proposed AdaFGL outperforms baselines by significant margins of 3.24\% and 5.57\% on community split and structure Non-iid split, respectively.
Few-shot node classification poses a significant challenge for Graph Neural Networks (GNNs) due to insufficient supervision and potential distribution shifts between labeled and unlabeled nodes. Self-training has emerged as a widely popular framework to leverage the abundance of unlabeled data, which expands the training set by assigning pseudo-labels to selected unlabeled nodes. Efforts have been made to develop various selection strategies based on confidence, information gain, etc. However, none of these methods takes into account the distribution shift between the training and testing node sets. The pseudo-labeling step may amplify this shift and even introduce new ones, hindering the effectiveness of self-training. Therefore, in this work, we explore the potential of explicitly bridging the distribution shift between the expanded training set and test set during self-training. To this end, we propose a novel Distribution-Consistent Graph Self-Training (DC-GST) framework to identify pseudo-labeled nodes that are both informative and capable of redeeming the distribution discrepancy and formulate it as a differentiable optimization task. A distribution-shift-aware edge predictor is further adopted to augment the graph and increase the model's generalizability in assigning pseudo labels. We evaluate our proposed method on four publicly available benchmark datasets and extensive experiments demonstrate that our framework consistently outperforms state-of-the-art baselines.
Graph Neural Networks (GNNs) have shown considerable effectiveness in a variety of graph learning tasks, particularly those based on the message-passing approach in recent years. However, their performance is often constrained by a limited receptive field, a challenge that becomes more acute in the presence of sparse graphs. In light of the power series, which possesses infinite expansion capabilities, we propose a novel Graph Power Filter Neural Network (GPFN) that enhances node classification by employing a power series graph filter to augment the receptive field. Concretely, our GPFN designs a new way to build a graph filter with an infinite receptive field based on the convergence power series, which can be analyzed in the spectral and spatial domains. Besides, we theoretically prove that our GPFN is a general framework that can integrate any power series and capture long-range dependencies. Finally, experimental results on three datasets demonstrate the superiority of our GPFN over state-of-the-art baselines.
Whilst spectral Graph Neural Networks (GNNs) are theoretically well-founded in the spectral domain, their practical reliance on polynomial approximation implies a profound linkage to the spatial domain. As previous studies rarely examine spectral GNNs from the spatial perspective, their spatial-domain interpretability remains elusive, e.g., what information is essentially encoded by spectral GNNs in the spatial domain? In this paper, to answer this question, we establish a theoretical connection between spectral filtering and spatial aggregation, unveiling an intrinsic interaction that spectral filtering implicitly leads the original graph to an adapted new graph, explicitly computed for spatial aggregation. Both theoretical and empirical investigations reveal that the adapted new graph not only exhibits non-locality but also accommodates signed edge weights to reflect label consistency among nodes. These findings thus highlight the interpretable role of spectral GNNs in the spatial domain and inspire us to rethink graph spectral filters beyond the fixed-order polynomials, which neglect global information. Built upon the theoretical findings, we revisit the state-of-the-art spectral GNNs and propose a novel Spatially Adaptive Filtering (SAF) framework, which leverages the adapted new graph by spectral filtering for an auxiliary non-local aggregation. Notably, our proposed SAF comprehensively models both node similarity and dissimilarity from a global perspective, therefore alleviating persistent deficiencies of GNNs related to long-range dependencies and graph heterophily. Extensive experiments over 13 node classification benchmarks demonstrate the superiority of our proposed framework to the state-of-the-art models.
We present a novel graph Transformer generative adversarial network (GTGAN) to learn effective graph node relations in an end-to-end fashion for challenging graph-constrained architectural layout generation tasks. The proposed graph-Transformer-based generator includes a novel graph Transformer encoder that combines graph convolutions and self-attentions in a Transformer to model both local and global interactions across connected and non-connected graph nodes. Specifically, the proposed connected node attention (CNA) and non-connected node attention (NNA) aim to capture the global relations across connected nodes and non-connected nodes in the input graph, respectively. The proposed graph modeling block (GMB) aims to exploit local vertex interactions based on a house layout topology. Moreover, we propose a new node classification-based discriminator to preserve the high-level semantic and discriminative node features for different house components. To maintain the relative spatial relationships between ground truth and predicted graphs, we also propose a novel graph-based cycle-consistency loss. Finally, we propose a novel self-guided pre-training method for graph representation learning. This approach involves simultaneous masking of nodes and edges at an elevated mask ratio (i.e., 40%) and their subsequent reconstruction using an asymmetric graph-centric autoencoder architecture. This method markedly improves the model's learning proficiency and expediency. Experiments on three challenging graph-constrained architectural layout generation tasks (i.e., house layout generation, house roof generation, and building layout generation) with three public datasets demonstrate the effectiveness of the proposed method in terms of objective quantitative scores and subjective visual realism. New state-of-the-art results are established by large margins on these three tasks.
The integration of Spiking Neural Networks (SNNs) and Graph Neural Networks (GNNs) is gradually attracting attention due to the low power consumption and high efficiency in processing the non-Euclidean data represented by graphs. However, as a common problem, dynamic graph representation learning faces challenges such as high complexity and large memory overheads. Current work often uses SNNs instead of Recurrent Neural Networks (RNNs) by using binary features instead of continuous ones for efficient training, which would overlooks graph structure information and leads to the loss of details during propagation. Additionally, optimizing dynamic spiking models typically requires propagation of information across time steps, which increases memory requirements. To address these challenges, we present a framework named \underline{Dy}namic \underline{S}p\underline{i}king \underline{G}raph \underline{N}eural Networks (\method{}). To mitigate the information loss problem, \method{} propagates early-layer information directly to the last layer for information compensation. To accommodate the memory requirements, we apply the implicit differentiation on the equilibrium state, which does not rely on the exact reverse of the forward computation. While traditional implicit differentiation methods are usually used for static situations, \method{} extends it to the dynamic graph setting. Extensive experiments on three large-scale real-world dynamic graph datasets validate the effectiveness of \method{} on dynamic node classification tasks with lower computational costs.
Graph neural networks (GNN) are a powerful tool for combining imaging and non-imaging medical information for node classification tasks. Cross-network node classification extends GNN techniques to account for domain drift, allowing for node classification on an unlabeled target network. In this paper we present OTGCN, a powerful, novel approach to cross-network node classification. This approach leans on concepts from graph convolutional networks to harness insights from graph data structures while simultaneously applying strategies rooted in optimal transport to correct for the domain drift that can occur between samples from different data collection sites. This blended approach provides a practical solution for scenarios with many distinct forms of data collected across different locations and equipment. We demonstrate the effectiveness of this approach at classifying Autism Spectrum Disorder subjects using a blend of imaging and non-imaging data.
Many aspects of graphs have been studied in depth. However, forecasting the structure of a graph at future time steps incorporating unseen, new nodes and edges has not gained much attention. In this paper, we present such an approach. Using a time series of graphs, we forecast graphs at future time steps. We use time series forecasting methods to predict the node degree at future time points and combine these forecasts with flux balance analysis -- a linear programming method used in biochemistry -- to obtain the structure of future graphs. We evaluate this approach using synthetic and real-world datasets and demonstrate its utility and applicability.