Graph Neural Networks (GNNs) have achieved state-of-the-art results in node classification tasks. However, most improvements are in multi-class classification, with less focus on the cases where each node could have multiple labels. The first challenge in studying multi-label node classification is the scarcity of publicly available datasets. To address this, we collected and released three real-world biological datasets and developed a multi-label graph generator with tunable properties. We also argue that traditional notions of homophily and heterophily do not apply well to multi-label scenarios. Therefore, we define homophily and Cross-Class Neighborhood Similarity for multi-label classification and investigate $9$ collected multi-label datasets. Lastly, we conducted a large-scale comparative study with $8$ methods across nine datasets to evaluate current progress in multi-label node classification. We release our code at \url{https://github.com/Tianqi-py/MLGNC}.
In terms of accuracy, Graph Neural Networks (GNNs) are the best architectural choice for the node classification task. Their drawback in real-world deployment is the latency that emerges from the neighbourhood processing operation. One solution to the latency issue is to perform knowledge distillation from a trained GNN to a Multi-Layer Perceptron (MLP), where the MLP processes only the features of the node being classified (and possibly some pre-computed structural information). However, the performance of such MLPs in both transductive and inductive settings remains inconsistent for existing knowledge distillation techniques. We propose to address the performance concerns by using a specially-designed student model instead of an MLP. Our model, named Routing-by-Memory (RbM), is a form of Mixture-of-Experts (MoE), with a design that enforces expert specialization. By encouraging each expert to specialize on a certain region on the hidden representation space, we demonstrate experimentally that it is possible to derive considerably more consistent performance across multiple datasets. Code available at https://github.com/Rufaim/routing-by-memory.
Graph Neural Networks (GNNs) have become pivotal tools for a range of graph-based learning tasks. Notably, most current GNN architectures operate under the assumption of homophily, whether explicitly or implicitly. While this underlying assumption is frequently adopted, it is not universally applicable, which can result in potential shortcomings in learning effectiveness. In this paper, \textbf{for the first time}, we transfer the prevailing concept of ``one node one receptive field" to the heterophilic graph. By constructing a proxy label predictor, we enable each node to possess a latent prediction distribution, which assists connected nodes in determining whether they should aggregate their associated neighbors. Ultimately, every node can have its own unique aggregation hop and pattern, much like each snowflake is unique and possesses its own characteristics. Based on observations, we innovatively introduce the Heterophily Snowflake Hypothesis and provide an effective solution to guide and facilitate research on heterophilic graphs and beyond. We conduct comprehensive experiments including (1) main results on 10 graphs with varying heterophily ratios across 10 backbones; (2) scalability on various deep GNN backbones (SGC, JKNet, etc.) across various large number of layers (2,4,6,8,16,32 layers); (3) comparison with conventional snowflake hypothesis; (4) efficiency comparison with existing graph pruning algorithms. Our observations show that our framework acts as a versatile operator for diverse tasks. It can be integrated into various GNN frameworks, boosting performance in-depth and offering an explainable approach to choosing the optimal network depth. The source code is available at \url{https://github.com/bingreeky/HeteroSnoH}.
Subgraph federated learning (SFL) is a research methodology that has gained significant attention for its potential to handle distributed graph-structured data. In SFL, the local model comprises graph neural networks (GNNs) with a partial graph structure. However, some SFL models have overlooked the significance of missing cross-subgraph edges, which can lead to local GNNs being unable to message-pass global representations to other parties' GNNs. Moreover, existing SFL models require substantial labeled data, which limits their practical applications. To overcome these limitations, we present a novel SFL framework called FedMpa that aims to learn cross-subgraph node representations. FedMpa first trains a multilayer perceptron (MLP) model using a small amount of data and then propagates the federated feature to the local structures. To further improve the embedding representation of nodes with local subgraphs, we introduce the FedMpae method, which reconstructs the local graph structure with an innovation view that applies pooling operation to form super-nodes. Our extensive experiments on six graph datasets demonstrate that FedMpa is highly effective in node classification. Furthermore, our ablation experiments verify the effectiveness of FedMpa.
The integration of Graph Neural Networks (GNNs) and Neural Ordinary and Partial Differential Equations has been extensively studied in recent years. GNN architectures powered by neural differential equations allow us to reason about their behavior, and develop GNNs with desired properties such as controlled smoothing or energy conservation. In this paper we take inspiration from Turing instabilities in a Reaction Diffusion (RD) system of partial differential equations, and propose a novel family of GNNs based on neural RD systems. We \textcolor{black}{demonstrate} that our RDGNN is powerful for the modeling of various data types, from homophilic, to heterophilic, and spatio-temporal datasets. We discuss the theoretical properties of our RDGNN, its implementation, and show that it improves or offers competitive performance to state-of-the-art methods.
The task of graph node classification is often approached by utilizing a local Graph Neural Network (GNN), that learns only local information from the node input features and their adjacency. In this paper, we propose to improve the performance of node classification GNNs by utilizing both global and local information, specifically by learning label- and node- features. We therefore call our method Global-Local-GNN (GLGNN). To learn proper label features, for each label, we maximize the similarity between its features and nodes features that belong to the label, while maximizing the distance between nodes that do not belong to the considered label. We then use the learnt label features to predict the node classification map. We demonstrate our GLGNN using three different GNN backbones, and show that our approach improves baseline performance, revealing the importance of global information utilization for node classification.
In this paper, we tackle a new problem of \textit{multi-source unsupervised domain adaptation (MSUDA) for graphs}, where models trained on annotated source domains need to be transferred to the unsupervised target graph for node classification. Due to the discrepancy in distribution across domains, the key challenge is how to select good source instances and how to adapt the model. Diverse graph structures further complicate this problem, rendering previous MSUDA approaches less effective. In this work, we present the framework Selective Multi-source Adaptation for Graph ({\method}), with a graph-modeling-based domain selector, a sub-graph node selector, and a bi-level alignment objective for the adaptation. Concretely, to facilitate the identification of informative source data, the similarity across graphs is disentangled and measured with the transferability of a graph-modeling task set, and we use it as evidence for source domain selection. A node selector is further incorporated to capture the variation in transferability of nodes within the same source domain. To learn invariant features for adaptation, we align the target domain to selected source data both at the embedding space by minimizing the optimal transport distance and at the classification level by distilling the label function. Modules are explicitly learned to select informative source data and conduct the alignment in virtual training splits with a meta-learning strategy. Experimental results on five graph datasets show the effectiveness of the proposed method.
Heterogeneous graphs have attracted a lot of research interests recently due to the success for representing complex real-world systems. However, existing methods have two pain points in embedding them into low-dimensional spaces: the mixing of structural and semantic information, and the distributional mismatch between data and embedding spaces. These two challenges require representation methods to consider the global and partial data distributions while unmixing the information. Therefore, in this paper, we propose $\text{Dis-H}^2\text{GCN}$, a Disentangled Hyperbolic Heterogeneous Graph Convolutional Network. On the one hand, we leverage the mutual information minimization and discrimination maximization constraints to disentangle the semantic features from comprehensively learned representations by independent message propagation for each edge type, away from the pure structural features. On the other hand, the entire model is constructed upon the hyperbolic geometry to narrow the gap between data distributions and representing spaces. We evaluate our proposed $\text{Dis-H}^2\text{GCN}$ on five real-world heterogeneous graph datasets across two downstream tasks: node classification and link prediction. The results demonstrate its superiority over state-of-the-art methods, showcasing the effectiveness of our method in disentangling and representing heterogeneous graph data in hyperbolic spaces.
Recent years have witnessed the remarkable success of applying Graph machine learning (GML) to node/graph classification and link prediction. However, edge classification task that enjoys numerous real-world applications such as social network analysis and cybersecurity, has not seen significant advancement. To address this gap, our study pioneers a comprehensive approach to edge classification. We identify a novel `Topological Imbalance Issue', which arises from the skewed distribution of edges across different classes, affecting the local subgraph of each edge and harming the performance of edge classifications. Inspired by the recent studies in node classification that the performance discrepancy exists with varying local structural patterns, we aim to investigate if the performance discrepancy in topological imbalanced edge classification can also be mitigated by characterizing the local class distribution variance. To overcome this challenge, we introduce Topological Entropy (TE), a novel topological-based metric that measures the topological imbalance for each edge. Our empirical studies confirm that TE effectively measures local class distribution variance, and indicate that prioritizing edges with high TE values can help address the issue of topological imbalance. Based on this, we develop two strategies - Topological Reweighting and TE Wedge-based Mixup - to focus training on (synthetic) edges based on their TEs. While topological reweighting directly manipulates training edge weights according to TE, our wedge-based mixup interpolates synthetic edges between high TE wedges. Ultimately, we integrate these strategies into a novel topological imbalance strategy for edge classification: TopoEdge. Through extensive experiments, we demonstrate the efficacy of our proposed strategies on newly curated datasets and thus establish a new benchmark for (imbalanced) edge classification.
We consider the problem of \textit{true} open-world semi-supervised node classification, in which nodes in a graph either belong to known or new classes, with the latter not present during training. Existing methods detect and reject new classes but fail to distinguish between different new classes. We adapt existing methods and show they do not solve the problem sufficiently. We introduce a novel end-to-end approach for classification into known classes and new classes based on class prototypes, which we call Prototypical Open-World Learning for Node Classification (POWN). Our method combines graph semi-supervised learning, self-supervised learning, and pseudo-labeling to learn prototype representations of new classes in a zero-shot way. In contrast to existing solutions from the vision domain, POWN does not require data augmentation techniques for node classification. Experiments on benchmark datasets demonstrate the effectiveness of POWN, where it outperforms baselines by up to $20\%$ accuracy on the small and up to $30\%$ on the large datasets. Source code is available at https://github.com/Bobowner/POWN.
Graph Neural Networks (GNNs) have achieved promising results in tasks such as node classification and graph classification. However, recent studies reveal that GNNs are vulnerable to backdoor attacks, posing a significant threat to their real-world adoption. Despite initial efforts to defend against specific graph backdoor attacks, there is no work on defending against various types of backdoor attacks where generated triggers have different properties. Hence, we first empirically verify that prediction variance under edge dropping is a crucial indicator for identifying poisoned nodes. With this observation, we propose using random edge dropping to detect backdoors and theoretically show that it can efficiently distinguish poisoned nodes from clean ones. Furthermore, we introduce a novel robust training strategy to efficiently counteract the impact of the triggers. Extensive experiments on real-world datasets show that our framework can effectively identify poisoned nodes, significantly degrade the attack success rate, and maintain clean accuracy when defending against various types of graph backdoor attacks with different properties.
Graph pooling has gained attention for its ability to obtain effective node and graph representations for various downstream tasks. Despite the recent surge in graph pooling approaches, there is a lack of standardized experimental settings and fair benchmarks to evaluate their performance. To address this issue, we have constructed a comprehensive benchmark that includes 17 graph pooling methods and 28 different graph datasets. This benchmark systematically assesses the performance of graph pooling methods in three dimensions, i.e., effectiveness, robustness, and generalizability. We first evaluate the performance of these graph pooling approaches across different tasks including graph classification, graph regression and node classification. Then, we investigate their performance under potential noise attacks and out-of-distribution shifts in real-world scenarios. We also involve detailed efficiency analysis, backbone analysis, parameter analysis and visualization to provide more evidence. Extensive experiments validate the strong capability and applicability of graph pooling approaches in various scenarios, which can provide valuable insights and guidance for deep geometric learning research. The source code of our benchmark is available at https://github.com/goose315/Graph_Pooling_Benchmark.
Graph Transformers (GTs) have recently emerged as popular alternatives to traditional message-passing Graph Neural Networks (GNNs), due to their theoretically superior expressiveness and impressive performance reported on standard node classification benchmarks, often significantly outperforming GNNs. In this paper, we conduct a thorough empirical analysis to reevaluate the performance of three classic GNN models (GCN, GAT, and GraphSAGE) against GTs. Our findings suggest that the previously reported superiority of GTs may have been overstated due to suboptimal hyperparameter configurations in GNNs. Remarkably, with slight hyperparameter tuning, these classic GNN models achieve state-of-the-art performance, matching or even exceeding that of recent GTs across 17 out of the 18 diverse datasets examined. Additionally, we conduct detailed ablation studies to investigate the influence of various GNN configurations, such as normalization, dropout, residual connections, and network depth, on node classification performance. Our study aims to promote a higher standard of empirical rigor in the field of graph machine learning, encouraging more accurate comparisons and evaluations of model capabilities.
Foundation Models (FMs) serve as a general class for the development of artificial intelligence systems, offering broad potential for generalization across a spectrum of downstream tasks. Despite extensive research into self-supervised learning as the cornerstone of FMs, several outstanding issues persist in Graph Foundation Models that rely on graph self-supervised learning, namely: 1) Homogenization. The extent of generalization capability on downstream tasks remains unclear. 2) Scalability. It is unknown how effectively these models can scale to large datasets. 3) Efficiency. The training time and memory usage of these models require evaluation. 4) Training Stop Criteria. Determining the optimal stopping strategy for pre-training across multiple tasks to maximize performance on downstream tasks. To address these questions, we have constructed a rigorous benchmark that thoroughly analyzes and studies the generalization and scalability of self-supervised Graph Neural Network (GNN) models. Regarding generalization, we have implemented and compared the performance of various self-supervised GNN models, trained to generate node representations, across tasks such as node classification, link prediction, and node clustering. For scalability, we have compared the performance of various models after training using full-batch and mini-batch strategies. Additionally, we have assessed the training efficiency of these models by conducting experiments to test their GPU memory usage and throughput. Through these experiments, we aim to provide insights to motivate future research. The code for this benchmark is publicly available at https://github.com/NYUSHCS/GraphFM.
Node embedding algorithms produce low-dimensional latent representations of nodes in a graph. These embeddings are often used for downstream tasks, such as node classification and link prediction. In this paper, we investigate the following two questions: (Q1) Can we explain each embedding dimension with human-understandable graph features (e.g. degree, clustering coefficient and PageRank). (Q2) How can we modify existing node embedding algorithms to produce embeddings that can be easily explained by human-understandable graph features? We find that the answer to Q1 is yes and introduce a new framework called XM (short for eXplain eMbedding) to answer Q2. A key aspect of XM involves minimizing the nuclear norm of the generated explanations. We show that by minimizing the nuclear norm, we minimize the lower bound on the entropy of the generated explanations. We test XM on a variety of real-world graphs and show that XM not only preserves the performance of existing node embedding methods, but also enhances their explainability.
Graph Convolutional Networks (GCN) are Graph Neural Networks where the convolutions are applied over a graph. In contrast to Convolutional Neural Networks, GCN's are designed to perform inference on graphs, where the number of nodes can vary, and the nodes are unordered. In this study, we address two important challenges related to GCNs: i) oversmoothing; and ii) the utilization of node relational properties (i.e., heterophily and homophily). Oversmoothing is the degradation of the discriminative capacity of nodes as a result of repeated aggregations. Heterophily is the tendency for nodes of different classes to connect, whereas homophily is the tendency of similar nodes to connect. We propose a new strategy for addressing these challenges in GCNs based on Transfer Entropy (TE), which measures of the amount of directed transfer of information between two time varying nodes. Our findings indicate that using node heterophily and degree information as a node selection mechanism, along with feature-based TE calculations, enhances accuracy across various GCN models. Our model can be easily modified to improve classification accuracy of a GCN model. As a trade off, this performance boost comes with a significant computational overhead when the TE is computed for many graph nodes.
This paper addresses the challenge of incremental learning in growing graphs with increasingly complex tasks. The goal is to continually train a graph model to handle new tasks while retaining its inference ability on previous tasks. Existing methods usually neglect the importance of memory diversity, limiting in effectively selecting high-quality memory from previous tasks and remembering broad previous knowledge within the scarce memory on graphs. To address that, we introduce a novel holistic Diversified Memory Selection and Generation (DMSG) framework for incremental learning in graphs, which first introduces a buffer selection strategy that considers both intra-class and inter-class diversities, employing an efficient greedy algorithm for sampling representative training nodes from graphs into memory buffers after learning each new task. Then, to adequately rememorize the knowledge preserved in the memory buffer when learning new tasks, we propose a diversified memory generation replay method. This method first utilizes a variational layer to generate the distribution of buffer node embeddings and sample synthesized ones for replaying. Furthermore, an adversarial variational embedding learning method and a reconstruction-based decoder are proposed to maintain the integrity and consolidate the generalization of the synthesized node embeddings, respectively. Finally, we evaluate our model on node classification tasks involving increasing class numbers. Extensive experimental results on publicly accessible datasets demonstrate the superiority of DMSG over state-of-the-art methods.
Graph neural networks based on message-passing mechanisms have achieved advanced results in graph classification tasks. However, their generalization performance degrades when noisy labels are present in the training data. Most existing noisy labeling approaches focus on the visual domain or graph node classification tasks and analyze the impact of noisy labels only from a utility perspective. Unlike existing work, in this paper, we measure the effects of noise labels on graph classification from data privacy and model utility perspectives. We find that noise labels degrade the model's generalization performance and enhance the ability of membership inference attacks on graph data privacy. To this end, we propose the robust graph neural network approach with noisy labeled graph classification. Specifically, we first accurately filter the noisy samples by high-confidence samples and the first feature principal component vector of each class. Then, the robust principal component vectors and the model output under data augmentation are utilized to achieve noise label correction guided by dual spatial information. Finally, supervised graph contrastive learning is introduced to enhance the embedding quality of the model and protect the privacy of the training graph data. The utility and privacy of the proposed method are validated by comparing twelve different methods on eight real graph classification datasets. Compared with the state-of-the-art methods, the RGLC method achieves at most and at least 7.8% and 0.8% performance gain at 30% noisy labeling rate, respectively, and reduces the accuracy of privacy attacks to below 60%.
In recent years, graph neural networks (GNNs) have emerged as a potent tool for learning on graph-structured data and won fruitful successes in varied fields. The majority of GNNs follow the message-passing paradigm, where representations of each node are learned by recursively aggregating features of its neighbors. However, this mechanism brings severe over-smoothing and efficiency issues over high-degree graphs (HDGs), wherein most nodes have dozens (or even hundreds) of neighbors, such as social networks, transaction graphs, power grids, etc. Additionally, such graphs usually encompass rich and complex structure semantics, which are hard to capture merely by feature aggregations in GNNs. Motivated by the above limitations, we propose TADA, an efficient and effective front-mounted data augmentation framework for GNNs on HDGs. Under the hood, TADA includes two key modules: (i) feature expansion with structure embeddings, and (ii) topology- and attribute-aware graph sparsification. The former obtains augmented node features and enhanced model capacity by encoding the graph structure into high-quality structure embeddings with our highly-efficient sketching method. Further, by exploiting task-relevant features extracted from graph structures and attributes, the second module enables the accurate identification and reduction of numerous redundant/noisy edges from the input graph, thereby alleviating over-smoothing and facilitating faster feature aggregations over HDGs. Empirically, TADA considerably improves the predictive performance of mainstream GNN models on 8 real homophilic/heterophilic HDGs in terms of node classification, while achieving efficient training and inference processes.
Graph Neural Networks (GNNs) have become invaluable intellectual property in graph-based machine learning. However, their vulnerability to model stealing attacks when deployed within Machine Learning as a Service (MLaaS) necessitates robust Ownership Demonstration (OD) techniques. Watermarking is a promising OD framework for Deep Neural Networks, but existing methods fail to generalize to GNNs due to the non-Euclidean nature of graph data. Previous works on GNN watermarking have primarily focused on node and graph classification, overlooking Link Prediction (LP). In this paper, we propose GENIE (watermarking Graph nEural Networks for lInk prEdiction), the first-ever scheme to watermark GNNs for LP. GENIE creates a novel backdoor for both node-representation and subgraph-based LP methods, utilizing a unique trigger set and a secret watermark vector. Our OD scheme is equipped with Dynamic Watermark Thresholding (DWT), ensuring high verification probability (>99.99%) while addressing practical issues in existing watermarking schemes. We extensively evaluate GENIE across 4 model architectures (i.e., SEAL, GCN, GraphSAGE and NeoGNN) and 7 real-world datasets. Furthermore, we validate the robustness of GENIE against 11 state-of-the-art watermark removal techniques and 3 model extraction attacks. We also show GENIE's resilience against ownership piracy attacks. Finally, we discuss a defense strategy to counter adaptive attacks against GENIE.