Graph out-of-distribution (OOD) generalization remains a major challenge in graph learning since graph neural networks (GNNs) often suffer from severe performance degradation under distribution shifts. Invariant learning, aiming to extract invariant features across varied distributions, has recently emerged as a promising approach for OOD generation. Despite the great success of invariant learning in OOD problems for Euclidean data (i.e., images), the exploration within graph data remains constrained by the complex nature of graphs. Existing studies, such as data augmentation or causal intervention, either suffer from disruptions to invariance during the graph manipulation process or face reliability issues due to a lack of supervised signals for causal parts. In this work, we propose a novel framework, called Invariant Graph Learning based on Information bottleneck theory (InfoIGL), to extract the invariant features of graphs and enhance models' generalization ability to unseen distributions. Specifically, InfoIGL introduces a redundancy filter to compress task-irrelevant information related to environmental factors. Cooperating with our designed multi-level contrastive learning, we maximize the mutual information among graphs of the same class in the downstream classification tasks, preserving invariant features for prediction to a great extent. An appealing feature of InfoIGL is its strong generalization ability without depending on supervised signal of invariance. Experiments on both synthetic and real-world datasets demonstrate that our method achieves state-of-the-art performance under OOD generalization for graph classification tasks. The source code is available at https://github.com/maowenyu-11/InfoIGL.
Recent research on the robustness of Graph Neural Networks (GNNs) under noises or attacks has attracted great attention due to its importance in real-world applications. Most previous methods explore a single noise source, recovering corrupt node embedding by reliable structures bias or developing structure learning with reliable node features. However, the noises and attacks may come from both structures and features in graphs, making the graph denoising a dilemma and challenging problem. In this paper, we develop a unified graph denoising (UGD) framework to unravel the deadlock between structure and feature denoising. Specifically, a high-order neighborhood proximity evaluation method is proposed to recognize noisy edges, considering features may be perturbed simultaneously. Moreover, we propose to refine noisy features with reconstruction based on a graph auto-encoder. An iterative updating algorithm is further designed to optimize the framework and acquire a clean graph, thus enabling robust graph learning for downstream tasks. Our UGD framework is self-supervised and can be easily implemented as a plug-and-play module. We carry out extensive experiments, which proves the effectiveness and advantages of our method. Code is avalaible at https://github.com/YoungTimmy/UGD.
Rethink convolution-based graph neural networks (GNN) -- they characteristically suffer from limited expressiveness, over-smoothing, and over-squashing, and require specialized sparse kernels for efficient computation. Here, we design a simple graph learning module entirely free of convolution operators, coined random walk with unifying memory (RUM) neural network, where an RNN merges the topological and semantic graph features along the random walks terminating at each node. Relating the rich literature on RNN behavior and graph topology, we theoretically show and experimentally verify that RUM attenuates the aforementioned symptoms and is more expressive than the Weisfeiler-Lehman (WL) isomorphism test. On a variety of node- and graph-level classification and regression tasks, RUM not only achieves competitive performance, but is also robust, memory-efficient, scalable, and faster than the simplest convolutional GNNs.
Knowledge Tracing aims to assess student learning states by predicting their performance in answering questions. Different from the existing research which utilizes fixed-length learning sequence to obtain the student states and regards KT as a static problem, this work is motivated by three dynamical characteristics: 1) The scales of students answering records are constantly growing; 2) The semantics of time intervals between the records vary; 3) The relationships between students, questions and concepts are evolving. The three dynamical characteristics above contain the great potential to revolutionize the existing knowledge tracing methods. Along this line, we propose a Dynamic Graph-based Knowledge Tracing model, namely DyGKT. In particular, a continuous-time dynamic question-answering graph for knowledge tracing is constructed to deal with the infinitely growing answering behaviors, and it is worth mentioning that it is the first time dynamic graph learning technology is used in this field. Then, a dual time encoder is proposed to capture long-term and short-term semantics among the different time intervals. Finally, a multiset indicator is utilized to model the evolving relationships between students, questions, and concepts via the graph structural feature. Numerous experiments are conducted on five real-world datasets, and the results demonstrate the superiority of our model. All the used resources are publicly available at https://github.com/PengLinzhi/DyGKT.
Continual graph learning (CGL) is an important and challenging task that aims to extend static GNNs to dynamic task flow scenarios. As one of the mainstream CGL methods, the experience replay (ER) method receives widespread attention due to its superior performance. However, existing ER methods focus on identifying samples by feature significance or topological relevance, which limits their utilization of comprehensive graph data. In addition, the topology-based ER methods only consider local topological information and add neighboring nodes to the buffer, which ignores the global topological information and increases memory overhead. To bridge these gaps, we propose a novel method called Feature-Topology Fusion-based Experience Replay (FTF-ER) to effectively mitigate the catastrophic forgetting issue with enhanced efficiency. Specifically, from an overall perspective to maximize the utilization of the entire graph data, we propose a highly complementary approach including both feature and global topological information, which can significantly improve the effectiveness of the sampled nodes. Moreover, to further utilize global topological information, we propose Hodge Potential Score (HPS) as a novel module to calculate the topological importance of nodes. HPS derives a global node ranking via Hodge decomposition on graphs, providing more accurate global topological information compared to neighbor sampling. By excluding neighbor sampling, HPS significantly reduces buffer storage costs for acquiring topological information and simultaneously decreases training time. Compared with state-of-the-art methods, FTF-ER achieves a significant improvement of 3.6% in AA and 7.1% in AF on the OGB-Arxiv dataset, demonstrating its superior performance in the class-incremental learning setting.
Summarizing web graphs is challenging due to the heterogeneity of the modeled information and its changes over time. We investigate the use of neural networks for lifelong graph summarization. Assuming we observe the web graph at a certain time, we train the networks to summarize graph vertices. We apply this trained network to summarize the vertices of the changed graph at the next point in time. Subsequently, we continue training and evaluating the network to perform lifelong graph summarization. We use the GNNs Graph-MLP and GraphSAINT, as well as an MLP baseline, to summarize the temporal graphs. We compare $1$-hop and $2$-hop summaries. We investigate the impact of reusing parameters from a previous snapshot by measuring the backward and forward transfer and the forgetting rate of the neural networks. Our extensive experiments on ten weekly snapshots of a web graph with over $100$M edges, sampled in 2012 and 2022, show that all networks predominantly use $1$-hop information to determine the summary, even when performing $2$-hop summarization. Due to the heterogeneity of web graphs, in some snapshots, the $2$-hop summary produces over ten times more vertex summaries than the $1$-hop summary. When using the network trained on the last snapshot from 2012 and applying it to the first snapshot of 2022, we observe a strong drop in accuracy. We attribute this drop over the ten-year time warp to the strongly increased heterogeneity of the web graph in 2022.
Node classification is an essential problem in graph learning. However, many models typically obtain unsatisfactory performance when applied to few-shot scenarios. Some studies have attempted to combine meta-learning with graph neural networks to solve few-shot node classification on graphs. Despite their promising performance, some limitations remain. First, they employ the node encoding mechanism of homophilic graphs to learn node embeddings, even in heterophilic graphs. Second, existing models based on meta-learning ignore the interference of randomness in the learning process. Third, they are trained using only limited labeled nodes within the specific task, without explicitly utilizing numerous unlabeled nodes. Finally, they treat almost all sampled tasks equally without customizing them for their uniqueness. To address these issues, we propose a novel framework for few-shot node classification called Meta-GPS++. Specifically, we first adopt an efficient method to learn discriminative node representations on homophilic and heterophilic graphs. Then, we leverage a prototype-based approach to initialize parameters and contrastive learning for regularizing the distribution of node embeddings. Moreover, we apply self-training to extract valuable information from unlabeled nodes. Additionally, we adopt S$^2$ (scaling & shifting) transformation to learn transferable knowledge from diverse tasks. The results on real-world datasets show the superiority of Meta-GPS++. Our code is available here.
We propose GLAudio: Graph Learning on Audio representation of the node features and the connectivity structure. This novel architecture propagates the node features through the graph network according to the discrete wave equation and then employs a sequence learning architecture to learn the target node function from the audio wave signal. This leads to a new paradigm of learning on graph-structured data, in which information propagation and information processing are separated into two distinct steps. We theoretically characterize the expressivity of our model, introducing the notion of the receptive field of a vertex, and investigate our model's susceptibility to over-smoothing and over-squashing both theoretically as well as experimentally on various graph datasets.
Dynamic link prediction is a critical task in the analysis of evolving networks, with applications ranging from recommender systems to economic exchanges. However, the concept of the temporal receptive field, which refers to the temporal context that models use for making predictions, has been largely overlooked and insufficiently analyzed in existing research. In this study, we present a comprehensive analysis of the temporal receptive field in dynamic graph learning. By examining multiple datasets and models, we formalize the role of temporal receptive field and highlight their crucial influence on predictive accuracy. Our results demonstrate that appropriately chosen temporal receptive field can significantly enhance model performance, while for some models, overly large windows may introduce noise and reduce accuracy. We conduct extensive benchmarking to validate our findings, ensuring that all experiments are fully reproducible. Code is available at https://github.com/ykrmm/BenchmarkTW .
Given partial measurements of a time-varying graph signal, we propose an algorithm to simultaneously estimate both the underlying graph topology and the missing measurements. The proposed algorithm operates by training an interpretable neural network, designed from the unrolling framework. The proposed technique can be used both as a graph learning and a graph signal reconstruction algorithm. This work enhances prior work in graph signal reconstruction by allowing the underlying graph to be unknown; and also builds on prior work in graph learning by tailoring the learned graph to the signal reconstruction task.
Lane topology, which is usually modeled by a centerline graph, is essential for high-level autonomous driving. For a high-quality graph, both topology connectivity and spatial continuity of centerline segments are critical. However, most of existing approaches pay more attention to connectivity while neglect the continuity. Such kind of centerline graph usually cause problem to planning of autonomous driving. To overcome this problem, we present an end-to-end network, CGNet, with three key modules: 1)Junction Aware Query Enhancement module, which provides positional prior to accurately predict junction points; 2)B\'ezier Space Connection module, which enforces continuity constraints on any two topologically connected segments in a B\'ezier space; 3) Iterative Topology Refinement module, which is a graph-based network with memory to iteratively refine the predicted topological connectivity. CGNet achieves state-of-the-art performance on both nuScenes and Argoverse2 datasets.
Mini-batch Graph Transformer (MGT), as an emerging graph learning model, has demonstrated significant advantages in semi-supervised node prediction tasks with improved computational efficiency and enhanced model robustness. However, existing methods for processing local information either rely on sampling or simple aggregation, which respectively result in the loss and squashing of critical neighbor information.Moreover, the limited number of nodes in each mini-batch restricts the model's capacity to capture the global characteristic of the graph. In this paper, we propose LGMformer, a novel MGT model that employs a two-stage augmented interaction strategy, transitioning from local to global perspectives, to address the aforementioned bottlenecks.The local interaction augmentation (LIA) presents a neighbor-target interaction Transformer (NTIformer) to acquire an insightful understanding of the co-interaction patterns between neighbors and the target node, resulting in a locally effective token list that serves as input for the MGT. In contrast, global interaction augmentation (GIA) adopts a cross-attention mechanism to incorporate entire graph prototypes into the target node epresentation, thereby compensating for the global graph information to ensure a more comprehensive perception. To this end, LGMformer achieves the enhancement of node representations under the MGT paradigm.Experimental results related to node classification on the ten benchmark datasets demonstrate the effectiveness of the proposed method. Our code is available at https://github.com/l-wd/LGMformer.
Mixup has shown considerable success in mitigating the challenges posed by limited labeled data in image classification. By synthesizing samples through the interpolation of features and labels, Mixup effectively addresses the issue of data scarcity. However, it has rarely been explored in graph learning tasks due to the irregularity and connectivity of graph data. Specifically, in node classification tasks, Mixup presents a challenge in creating connections for synthetic data. In this paper, we propose Geometric Mixup (GeoMix), a simple and interpretable Mixup approach leveraging in-place graph editing. It effectively utilizes geometry information to interpolate features and labels with those from the nearby neighborhood, generating synthetic nodes and establishing connections for them. We conduct theoretical analysis to elucidate the rationale behind employing geometry information for node Mixup, emphasizing the significance of locality enhancement-a critical aspect of our method's design. Extensive experiments demonstrate that our lightweight Geometric Mixup achieves state-of-the-art results on a wide variety of standard datasets with limited labeled data. Furthermore, it significantly improves the generalization capability of underlying GNNs across various challenging out-of-distribution generalization tasks. Our code is available at https://github.com/WtaoZhao/geomix.
Graph mining has become crucial in fields such as social science, finance, and cybersecurity. Many large-scale real-world networks exhibit both heterogeneity, where multiple node and edge types exist in the graph, and heterophily, where connected nodes may have dissimilar labels and attributes. However, existing benchmarks primarily focus on either heterophilic homogeneous graphs or homophilic heterogeneous graphs, leaving a significant gap in understanding how models perform on graphs with both heterogeneity and heterophily. To bridge this gap, we introduce H2GB, a large-scale node-classification graph benchmark that brings together the complexities of both the heterophily and heterogeneity properties of real-world graphs. H2GB encompasses 9 real-world datasets spanning 5 diverse domains, 28 baseline models, and a unified benchmarking library with a standardized data loader, evaluator, unified modeling framework, and an extensible framework for reproducibility. We establish a standardized workflow supporting both model selection and development, enabling researchers to easily benchmark graph learning methods. Extensive experiments across 28 baselines reveal that current methods struggle with heterophilic and heterogeneous graphs, underscoring the need for improved approaches. Finally, we present a new variant of the model, H2G-former, developed following our standardized workflow, that excels at this challenging benchmark. Both the benchmark and the framework are publicly available at Github and PyPI, with documentation hosted at https://junhongmit.github.io/H2GB.
Existing WSI analysis methods lie on the consensus that histopathological characteristics of tumors are significant guidance for cancer diagnostics. Particularly, as the evolution of cancers is a continuous process, the correlations and differences across various stages, anatomical locations and patients should be taken into account. However, recent research mainly focuses on the inner-contextual information in a single WSI, ignoring the correlations between slides. To verify whether introducing the slide inter-correlations can bring improvements to WSI representation learning, we propose a generic WSI analysis pipeline SlideGCD that considers the existing multi-instance learning (MIL) methods as the backbone and forge the WSI classification task as a node classification problem. More specifically, SlideGCD declares a node buffer that stores previous slide embeddings for subsequent extensive slide-based graph construction and conducts graph learning to explore the inter-correlations implied in the slide-based graph. Moreover, we frame the MIL classifier and graph learning into two parallel workflows and deploy the knowledge distillation to transfer the differentiable information to the graph neural network. The consistent performance boosting, brought by SlideGCD, of four previous state-of-the-art MIL methods is observed on two TCGA benchmark datasets. The code is available at https://github.com/HFUT-miaLab/SlideGCD.
Tripartite graph-based recommender systems markedly diverge from traditional models by recommending unique combinations such as user groups and item bundles. Despite their effectiveness, these systems exacerbate the longstanding cold-start problem in traditional recommender systems, because any number of user groups or item bundles can be formed among users or items. To address this issue, we introduce a Consistency and Discrepancy-based graph contrastive learning method for tripartite graph-based Recommendation. This approach leverages two novel meta-path-based metrics consistency and discrepancy to capture nuanced, implicit associations between the recommended objects and the recommendees. These metrics, indicative of high-order similarities, can be efficiently calculated with infinite graph convolutional networks layers under a multi-objective optimization framework, using the limit theory of GCN.
Graph classification benchmarks, vital for assessing and developing graph neural networks (GNNs), have recently been scrutinized, as simple methods like MLPs have demonstrated comparable performance. This leads to an important question: Do these benchmarks effectively distinguish the advancements of GNNs over other methodologies? If so, how do we quantitatively measure this effectiveness? In response, we first propose an empirical protocol based on a fair benchmarking framework to investigate the performance discrepancy between simple methods and GNNs. We further propose a novel metric to quantify the dataset effectiveness by considering both dataset complexity and model performance. To the best of our knowledge, our work is the first to thoroughly study and provide an explicit definition for dataset effectiveness in the graph learning area. Through testing across 16 real-world datasets, we found our metric to align with existing studies and intuitive assumptions. Finally, we explore the causes behind the low effectiveness of certain datasets by investigating the correlation between intrinsic graph properties and class labels, and we developed a novel technique supporting the correlation-controllable synthetic dataset generation. Our findings shed light on the current understanding of benchmark datasets, and our new platform could fuel the future evolution of graph classification benchmarks.
We present the MEEG dataset, a multi-modal collection of music-induced electroencephalogram (EEG) recordings designed to capture emotional responses to various musical stimuli across different valence and arousal levels. This public dataset facilitates an in-depth examination of brainwave patterns within musical contexts, providing a robust foundation for studying brain network topology during emotional processing. Leveraging the MEEG dataset, we introduce the Attention-based Temporal Learner with Dynamic Graph Neural Network (AT-DGNN), a novel framework for EEG-based emotion recognition. This model combines an attention mechanism with a dynamic graph neural network (DGNN) to capture intricate EEG dynamics. The AT-DGNN achieves state-of-the-art (SOTA) performance with an accuracy of 83.74% in arousal recognition and 86.01% in valence recognition, outperforming existing SOTA methods. Comparative analysis with traditional datasets, such as DEAP, further validates the model's effectiveness and underscores the potency of music as an emotional stimulus. This study advances graph-based learning methodology in brain-computer interfaces (BCI), significantly improving the accuracy of EEG-based emotion recognition. The MEEG dataset and source code are publicly available at https://github.com/xmh1011/AT-DGNN.
Peptides are essential in biological processes and therapeutics. In this study, we introduce Multi-Peptide, an innovative approach that combines transformer-based language models with Graph Neural Networks (GNNs) to predict peptide properties. We combine PeptideBERT, a transformer model tailored for peptide property prediction, with a GNN encoder to capture both sequence-based and structural features. By employing Contrastive Language-Image Pre-training (CLIP), Multi-Peptide aligns embeddings from both modalities into a shared latent space, thereby enhancing the model's predictive accuracy. Evaluations on hemolysis and nonfouling datasets demonstrate Multi-Peptide's robustness, achieving state-of-the-art 86.185% accuracy in hemolysis prediction. This study highlights the potential of multimodal learning in bioinformatics, paving the way for accurate and reliable predictions in peptide-based research and applications.
Federated graph learning collaboratively learns a global graph neural network with distributed graphs, where the non-independent and identically distributed property is one of the major challenges. Most relative arts focus on traditional distributed tasks like images and voices, incapable of graph structures. This paper firstly reveals that local client distortion is brought by both node-level semantics and graph-level structure. First, for node-level semantics, we find that contrasting nodes from distinct classes is beneficial to provide a well-performing discrimination. We pull the local node towards the global node of the same class and push it away from the global node of different classes. Second, we postulate that a well-structural graph neural network possesses similarity for neighbors due to the inherent adjacency relationships. However, aligning each node with adjacent nodes hinders discrimination due to the potential class inconsistency. We transform the adjacency relationships into the similarity distribution and leverage the global model to distill the relation knowledge into the local model, which preserves the structural information and discriminability of the local model. Empirical results on three graph datasets manifest the superiority of the proposed method over its counterparts.