Temporal graph is an abstraction for modeling dynamic systems that consist of evolving interaction elements. In this paper, we aim to solve an important yet neglected problem -- how to learn information from high-order neighbors in temporal graphs? -- to enhance the informativeness and discriminativeness for the learned node representations. We argue that when learning high-order information from temporal graphs, we encounter two challenges, i.e., computational inefficiency and over-smoothing, that cannot be solved by conventional techniques applied on static graphs. To remedy these deficiencies, we propose a temporal propagation-based graph neural network, namely TPGNN. To be specific, the model consists of two distinct components, i.e., propagator and node-wise encoder. The propagator is leveraged to propagate messages from the anchor node to its temporal neighbors within $k$-hop, and then simultaneously update the state of neighborhoods, which enables efficient computation, especially for a deep model. In addition, to prevent over-smoothing, the model compels the messages from $n$-hop neighbors to update the $n$-hop memory vector preserved on the anchor. The node-wise encoder adopts transformer architecture to learn node representations by explicitly learning the importance of memory vectors preserved on the node itself, that is, implicitly modeling the importance of messages from neighbors at different layers, thus mitigating the over-smoothing. Since the encoding process will not query temporal neighbors, we can dramatically save time consumption in inference. Extensive experiments on temporal link prediction and node classification demonstrate the superiority of TPGNN over state-of-the-art baselines in efficiency and robustness.
Training graph neural networks (GNNs) on large graphs is complex and extremely time consuming. This is attributed to overheads caused by sparse matrix multiplication, which are sidestepped when training multi-layer perceptrons (MLPs) with only node features. MLPs, by ignoring graph context, are simple and faster for graph data, however they usually sacrifice prediction accuracy, limiting their applications for graph data. We observe that for most message passing-based GNNs, we can trivially derive an analog MLP (we call this a PeerMLP) with an equivalent weight space, by setting the trainable parameters with the same shapes, making us curious about \textbf{\emph{how do GNNs using weights from a fully trained PeerMLP perform?}} Surprisingly, we find that GNNs initialized with such weights significantly outperform their PeerMLPs, motivating us to use PeerMLP training as a precursor, initialization step to GNN training. To this end, we propose an embarrassingly simple, yet hugely effective initialization method for GNN training acceleration, called MLPInit. Our extensive experiments on multiple large-scale graph datasets with diverse GNN architectures validate that MLPInit can accelerate the training of GNNs (up to 33X speedup on OGB-Products) and often improve prediction performance (e.g., up to $7.97\%$ improvement for GraphSAGE across $7$ datasets for node classification, and up to $17.81\%$ improvement across $4$ datasets for link prediction on metric Hits@10). The code is available at \href{https://github.com/snap-research/MLPInit-for-GNNs}.
We present Gradient Gating (G$^2$), a novel framework for improving the performance of Graph Neural Networks (GNNs). Our framework is based on gating the output of GNN layers with a mechanism for multi-rate flow of message passing information across nodes of the underlying graph. Local gradients are harnessed to further modulate message passing updates. Our framework flexibly allows one to use any basic GNN layer as a wrapper around which the multi-rate gradient gating mechanism is built. We rigorously prove that G$^2$ alleviates the oversmoothing problem and allows the design of deep GNNs. Empirical results are presented to demonstrate that the proposed framework achieves state-of-the-art performance on a variety of graph learning tasks, including on large-scale heterophilic graphs.
The graph neural network (GNN) models have presented impressive achievements in numerous machine learning tasks. However, many existing GNN models are shown to be vulnerable to adversarial attacks, which creates a stringent need to build robust GNN architectures. In this work, we propose a novel interpretable message passing scheme with adaptive structure (ASMP) to defend against adversarial attacks on graph structure. Layers in ASMP are derived based on optimization steps that minimize an objective function that learns the node feature and the graph structure simultaneously. ASMP is adaptive in the sense that the message passing process in different layers is able to be carried out over dynamically adjusted graphs. Such property allows more fine-grained handling of the noisy (or perturbed) graph structure and hence improves the robustness. Convergence properties of the ASMP scheme are theoretically established. Integrating ASMP with neural networks can lead to a new family of GNN models with adaptive structure (ASGNN). Extensive experiments on semi-supervised node classification tasks demonstrate that the proposed ASGNN outperforms the state-of-the-art GNN architectures in terms of classification performance under various adversarial attacks.
Graph contrastive learning (GCL), as an emerging self-supervised learning technique on graphs, aims to learn representations via instance discrimination. Its performance heavily relies on graph augmentation to reflect invariant patterns that are robust to small perturbations; yet it still remains unclear about what graph invariance GCL should capture. Recent studies mainly perform topology augmentations in a uniformly random manner in the spatial domain, ignoring its influence on the intrinsic structural properties embedded in the spectral domain. In this work, we aim to find a principled way for topology augmentations by exploring the invariance of graphs from the spectral perspective. We develop spectral augmentation which guides topology augmentations by maximizing the spectral change. Extensive experiments on both graph and node classification tasks demonstrate the effectiveness of our method in self-supervised representation learning. The proposed method also brings promising generalization capability in transfer learning, and is equipped with intriguing robustness property under adversarial attacks. Our study sheds light on a general principle for graph topology augmentation.
Graphs are used widely to model complex systems, and detecting anomalies in a graph is an important task in the analysis of complex systems. Graph anomalies are patterns in a graph that do not conform to normal patterns expected of the attributes and/or structures of the graph. In recent years, graph neural networks (GNNs) have been studied extensively and have successfully performed difficult machine learning tasks in node classification, link prediction, and graph classification thanks to the highly expressive capability via message passing in effectively learning graph representations. To solve the graph anomaly detection problem, GNN-based methods leverage information about the graph attributes (or features) and/or structures to learn to score anomalies appropriately. In this survey, we review the recent advances made in detecting graph anomalies using GNN models. Specifically, we summarize GNN-based methods according to the graph type (i.e., static and dynamic), the anomaly type (i.e., node, edge, subgraph, and whole graph), and the network architecture (e.g., graph autoencoder, graph convolutional network). To the best of our knowledge, this survey is the first comprehensive review of graph anomaly detection methods based on GNNs.
Graph Neural Networks (GNNs) have been generalized to process the heterogeneous graphs by various approaches. Unfortunately, these approaches usually model the heterogeneity via various complicated modules. This paper aims to propose a simple yet effective framework to assign adequate ability to the homogeneous GNNs to handle the heterogeneous graphs. Specifically, we propose Relation Embedding based Graph Neural Network (RE-GNN), which employs only one parameter per relation to embed the importance of distinct types of relations and node-type-specific self-loop connections. To optimize these relation embeddings and the model parameters simultaneously, a gradient scaling factor is proposed to constrain the embeddings to converge to suitable values. Besides, we interpret the proposed RE-GNN from two perspectives, and theoretically demonstrate that our RE-GCN possesses more expressive power than GTN (which is a typical heterogeneous GNN, and it can generate meta-paths adaptively). Extensive experiments demonstrate that our RE-GNN can effectively and efficiently handle the heterogeneous graphs and can be applied to various homogeneous GNNs.
In recent years, the node classification task in graph neural networks(GNNs) has developed rapidly, driving the development of research in various fields. However, there are a large number of class imbalances in the graph data, and there is a large gap between the number of different classes, resulting in suboptimal results in classification. Proposing a solution to the imbalance problem has become indispensable for the successful advancement of our downstream missions. Therefore, we start with the loss function and try to find a loss function that can effectively solve the imbalance of graph nodes to participate in the node classification task. thence, we introduce GHMC Loss into the graph neural networks to deal with difficult samples that are not marginal. Attenuate the loss contribution of marginal samples and simple samples. Experiments on multiple benchmarks show that our method can effectively deal with the class imbalance problem, and our method improves the accuracy by 3% compared to the traditional loss function.
We introduce De Bruijn Graph Neural Networks (DBGNNs), a novel time-aware graph neural network architecture for time-resolved data on dynamic graphs. Our approach accounts for temporal-topological patterns that unfold in the causal topology of dynamic graphs, which is determined by causal walks, i.e. temporally ordered sequences of links by which nodes can influence each other over time. Our architecture builds on multiple layers of higher-order De Bruijn graphs, an iterative line graph construction where nodes in a De Bruijn graph of order k represent walks of length k-1, while edges represent walks of length k. We develop a graph neural network architecture that utilizes De Bruijn graphs to implement a message passing scheme that follows a non-Markovian dynamics, which enables us to learn patterns in the causal topology of a dynamic graph. Addressing the issue that De Bruijn graphs with different orders k can be used to model the same data set, we further apply statistical model selection to determine the optimal graph topology to be used for message passing. An evaluation in synthetic and empirical data sets suggests that DBGNNs can leverage temporal patterns in dynamic graphs, which substantially improves the performance in a supervised node classification task.
Graph Neural Networks (GNNs) are popular machine learning methods for modeling graph data. A lot of GNNs perform well on homophily graphs while having unsatisfactory performance on heterophily graphs. Recently, some researchers turn their attention to designing GNNs for heterophily graphs by adjusting the message passing mechanism or enlarging the receptive field of the message passing. Different from existing works that mitigate the issues of heterophily from model design perspective, we propose to study heterophily graphs from an orthogonal perspective by rewiring the graph structure to reduce heterophily and making the traditional GNNs perform better. Through comprehensive empirical studies and analysis, we verify the potential of the rewiring methods. To fully exploit its potential, we propose a method named Deep Heterophily Graph Rewiring (DHGR) to rewire graphs by adding homophilic edges and pruning heterophilic edges. The detailed way of rewiring is determined by comparing the similarity of label/feature-distribution of node neighbors. Besides, we design a scalable implementation for DHGR to guarantee high efficiency. DHRG can be easily used as a plug-in module, i.e., a graph pre-processing step, for any GNNs, including both GNN for homophily and heterophily, to boost their performance on the node classification task. To the best of our knowledge, it is the first work studying graph rewiring for heterophily graphs. Extensive experiments on 11 public graph datasets demonstrate the superiority of our proposed methods.
While graph neural networks (GNNs) have been successful for node classification tasks and link prediction tasks in graph, learning graph-level representations still remains a challenge. For the graph-level representation, it is important to learn both representation of neighboring nodes, i.e., aggregation, and graph structural information. A number of graph pooling methods have been developed for this goal. However, most of the existing pooling methods utilize k-hop neighborhood without considering explicit structural information in a graph. In this paper, we propose Structure Prototype Guided Pooling (SPGP) that utilizes prior graph structures to overcome the limitation. SPGP formulates graph structures as learnable prototype vectors and computes the affinity between nodes and prototype vectors. This leads to a novel node scoring scheme that prioritizes informative nodes while encapsulating the useful structures of the graph. Our experimental results show that SPGP outperforms state-of-the-art graph pooling methods on graph classification benchmark datasets in both accuracy and scalability.
In the last two decades we are witnessing a huge increase of valuable big data structured in the form of graphs or networks. To apply traditional machine learning and data analytic techniques to such data it is necessary to transform graphs into vector-based representations that preserve the most essential structural properties of graphs. For this purpose, a large number of graph embedding methods have been proposed in the literature. Most of them produce general-purpose embeddings suitable for a variety of applications such as node clustering, node classification, graph visualisation and link prediction. In this paper, we propose two novel graph embedding algorithms based on random walks that are specifically designed for the node classification problem. Random walk sampling strategies of the proposed algorithms have been designed to pay special attention to hubs -- high-degree nodes that have the most critical role for the overall connectedness in large-scale graphs. The proposed methods are experimentally evaluated by analyzing the classification performance of three classification algorithms trained on embeddings of real-world networks. The obtained results indicate that our methods considerably improve the predictive power of examined classifiers compared to currently the most popular random walk method for generating general-purpose graph embeddings (node2vec).
Node embedding methods map network nodes to low dimensional vectors that can be subsequently used in a variety of downstream prediction tasks. The popularity of these methods has grown significantly in recent years, yet, their robustness to perturbations of the input data is still poorly understood. In this paper, we assess the empirical robustness of node embedding models to random and adversarial poisoning attacks. Our systematic evaluation covers representative embedding methods based on Skip-Gram, matrix factorization, and deep neural networks. We compare edge addition, deletion and rewiring attacks computed using network properties as well as node labels. We also investigate the performance of popular node classification attack baselines that assume full knowledge of the node labels. We report qualitative results via embedding visualization and quantitative results in terms of downstream node classification and network reconstruction performances. We find that node classification results are impacted more than network reconstruction ones, that degree-based and label-based attacks are on average the most damaging and that label heterophily can strongly influence attack performance.
Graph neural network (GNN) pre-training methods have been proposed to enhance the power of GNNs. Specifically, a GNN is first pre-trained on a large-scale unlabeled graph and then fine-tuned on a separate small labeled graph for downstream applications, such as node classification. One popular pre-training method is to mask out a proportion of the edges, and a GNN is trained to recover them. However, such a generative method suffers from graph mismatch. That is, the masked graph inputted to the GNN deviates from the original graph. To alleviate this issue, we propose DiP-GNN (Discriminative Pre-training of Graph Neural Networks). Specifically, we train a generator to recover identities of the masked edges, and simultaneously, we train a discriminator to distinguish the generated edges from the original graph's edges. In our framework, the graph seen by the discriminator better matches the original graph because the generator can recover a proportion of the masked edges. Extensive experiments on large-scale homogeneous and heterogeneous graphs demonstrate the effectiveness of the proposed framework.
Multimodal machine learning has been widely studied for the development of general intelligence. Recently, the remarkable multimodal algorithms, the Perceiver and Perceiver IO, show competitive results for diverse dataset domains and tasks. However, recent works, Perceiver and Perceiver IO, have focused on heterogeneous modalities, including image, text, and speech, and there are few research works for graph structured datasets. A graph is one of the most generalized dataset structures, and we can represent the other dataset, including images, text, and speech, as graph structured data. A graph has an adjacency matrix different from other dataset domains such as text and image, and it is not trivial to handle the topological information, relational information, and canonical positional information. In this study, we provide a Graph Perceiver IO, the Perceiver IO for the graph structured dataset. We keep the main structure of the Graph Perceiver IO as the Perceiver IO because the Perceiver IO already handles the diverse dataset well, except for the graph structured dataset. The Graph Perceiver IO is a general method, and it can handle diverse datasets such as graph structured data as well as text and images. Comparing the graph neural networks, the Graph Perceiver IO requires a lower complexity, and it can incorporate the local and global information efficiently. We show that Graph Perceiver IO shows competitive results for diverse graph-related tasks, including node classification, graph classification, and link prediction.
Homophily is a graph property describing the tendency of edges to connect similar nodes; the opposite is called heterophily. It is often believed that heterophilous graphs are challenging for standard message-passing graph neural networks (GNNs), and much effort has been put into developing efficient methods for this setting. However, there is no universally agreed-upon measure of homophily in the literature. In this work, we show that commonly used homophily measures have critical drawbacks preventing the comparison of homophily levels across different datasets. For this, we formalize desirable properties for a proper homophily measure and verify which measures satisfy which properties. In particular, we show that a measure that we call adjusted homophily satisfies more desirable properties than other popular homophily measures while being rarely used in graph machine learning literature. Then, we go beyond the homophily-heterophily dichotomy and propose a new characteristic that allows one to further distinguish different sorts of heterophily. The proposed label informativeness (LI) characterizes how much information a neighbor's label provides about a node's label. We prove that this measure satisfies important desirable properties. We also observe empirically that LI better agrees with GNN performance compared to homophily measures, which confirms that it is a useful characteristic of the graph structure.
We present evidence for the existence and effectiveness of adversarial attacks on graph neural networks (GNNs) that aim to degrade fairness. These attacks can disadvantage a particular subgroup of nodes in GNN-based node classification, where nodes of the underlying network have sensitive attributes, such as race or gender. We conduct qualitative and experimental analyses explaining how adversarial link injection impairs the fairness of GNN predictions. For example, an attacker can compromise the fairness of GNN-based node classification by injecting adversarial links between nodes belonging to opposite subgroups and opposite class labels. Our experiments on empirical datasets demonstrate that adversarial fairness attacks can significantly degrade the fairness of GNN predictions (attacks are effective) with a low perturbation rate (attacks are efficient) and without a significant drop in accuracy (attacks are deceptive). This work demonstrates the vulnerability of GNN models to adversarial fairness attacks. We hope our findings raise awareness about this issue in our community and lay a foundation for the future development of GNN models that are more robust to such attacks.
Video action segmentation have been widely applied in many fields. Most previous studies employed video-based vision models for this purpose. However, they often rely on a large receptive field, LSTM or Transformer methods to capture long-term dependencies within videos, leading to significant computational resource requirements. To address this challenge, graph-based model was proposed. However, previous graph-based models are less accurate. Hence, this study introduces a graph-structured approach named Semantic2Graph, to model long-term dependencies in videos, thereby reducing computational costs and raise the accuracy. We construct a graph structure of video at the frame-level. Temporal edges are utilized to model the temporal relations and action order within videos. Additionally, we have designed positive and negative semantic edges, accompanied by corresponding edge weights, to capture both long-term and short-term semantic relationships in video actions. Node attributes encompass a rich set of multi-modal features extracted from video content, graph structures, and label text, encompassing visual, structural, and semantic cues. To synthesize this multi-modal information effectively, we employ a graph neural network (GNN) model to fuse multi-modal features for node action label classification. Experimental results demonstrate that Semantic2Graph outperforms state-of-the-art methods in terms of performance, particularly on benchmark datasets such as GTEA and 50Salads. Multiple ablation experiments further validate the effectiveness of semantic features in enhancing model performance. Notably, the inclusion of semantic edges in Semantic2Graph allows for the cost-effective capture of long-term dependencies, affirming its utility in addressing the challenges posed by computational resource constraints in video-based vision models.
We investigate efficient learning from higher-order graph convolution and learning directly from adjacency matrices for node classification. We revisit the scaled graph residual network and remove ReLU activation from residual layers and apply a single weight matrix at each residual layer. We show that the resulting model lead to new graph convolution models as a polynomial of the normalized adjacency matrix, the residual weight matrix, and the residual scaling parameter. Additionally, we propose adaptive learning between directly graph polynomial convolution models and learning directly from the adjacency matrix. Furthermore, we propose fully adaptive models to learn scaling parameters at each residual layer. We show that generalization bounds of proposed methods are bounded as a polynomial of eigenvalue spectrum, scaling parameters, and upper bounds of residual weights. By theoretical analysis, we argue that the proposed models can obtain improved generalization bounds by limiting the higher-orders of convolutions and direct learning from the adjacency matrix. Using a wide set of real-data, we demonstrate that the proposed methods obtain improved accuracy for node-classification of non-homophilous graphs.
Graph embedding methods aim at finding useful graph representations by mapping nodes to a low-dimensional vector space. It is a task with important downstream applications, such as link prediction, graph reconstruction, data visualization, node classification, and language modeling. In recent years, the field of graph embedding has witnessed a shift from linear algebraic approaches towards local, gradient-based optimization methods combined with random walks and deep neural networks to tackle the problem of embedding large graphs. However, despite this improvement in the optimization tools, graph embedding methods are still generically designed in a way that is oblivious to the particularities of real-life networks. Indeed, there has been significant progress in understanding and modeling complex real-life networks in recent years. However, the obtained results have had a minor influence on the development of graph embedding algorithms. This paper aims to remedy this by designing a graph embedding method that takes advantage of recent valuable insights from the field of network science. More precisely, we present a novel graph embedding approach based on the popularity-similarity and local attraction paradigms. We evaluate the performance of the proposed approach on the link prediction task on a large number of real-life networks. We show, using extensive experimental analysis, that the proposed method outperforms state-of-the-art graph embedding algorithms. We also demonstrate its robustness to data scarcity and the choice of embedding dimensionality.