Recent studies attempted to utilize multilayer perceptrons (MLPs) to solve semisupervised node classification on graphs, by training a student MLP by knowledge distillation from a teacher graph neural network (GNN). While previous studies have focused mostly on training the student MLP by matching the output probability distributions between the teacher and student models during distillation, it has not been systematically studied how to inject the structural information in an explicit and interpretable manner. Inspired by GNNs that separate feature transformation $T$ and propagation $\Pi$, we re-frame the distillation process as making the student MLP learn both $T$ and $\Pi$. Although this can be achieved by applying the inverse propagation $\Pi^{-1}$ before distillation from the teacher, it still comes with a high computational cost from large matrix multiplications during training. To solve this problem, we propose Propagate & Distill (P&D), which propagates the output of the teacher before distillation, which can be interpreted as an approximate process of the inverse propagation. We demonstrate that P&D can readily improve the performance of the student MLP.
As a powerful framework for graph representation learning, Graph Neural Networks (GNNs) have garnered significant attention in recent years. However, to the best of our knowledge, there has been no formal analysis of the logical expressiveness of GNNs as Boolean node classifiers over multi-relational graphs, where each edge carries a specific relation type. In this paper, we investigate $\mathcal{FOC}_2$, a fragment of first-order logic with two variables and counting quantifiers. On the negative side, we demonstrate that the R$^2$-GNN architecture, which extends the local message passing GNN by incorporating global readout, fails to capture $\mathcal{FOC}_2$ classifiers in the general case. Nevertheless, on the positive side, we establish that R$^2$-GNNs models are equivalent to $\mathcal{FOC}_2$ classifiers under certain restricted yet reasonable scenarios. To address the limitations of R$^2$-GNNs regarding expressiveness, we propose a simple graph transformation technique, akin to a preprocessing step, which can be executed in linear time. This transformation enables R$^2$-GNNs to effectively capture any $\mathcal{FOC}_2$ classifiers when applied to the "transformed" input graph. Moreover, we extend our analysis of expressiveness and graph transformation to temporal graphs, exploring several temporal GNN architectures and providing an expressiveness hierarchy for them. To validate our findings, we implement R$^2$-GNNs and the graph transformation technique and conduct empirical tests in node classification tasks against various well-known GNN architectures that support multi-relational or temporal graphs. Our experimental results consistently demonstrate that R$^2$-GNN with the graph transformation outperforms the baseline methods on both synthetic and real-world datasets
Temporal hypergraphs provide a powerful paradigm for modeling time-dependent, higher-order interactions in complex systems. Representation learning for hypergraphs is essential for extracting patterns of the higher-order interactions that are critically important in real-world problems in social network analysis, neuroscience, finance, etc. However, existing methods are typically designed only for specific tasks or static hypergraphs. We present CAT-Walk, an inductive method that learns the underlying dynamic laws that govern the temporal and structural processes underlying a temporal hypergraph. CAT-Walk introduces a temporal, higher-order walk on hypergraphs, SetWalk, that extracts higher-order causal patterns. CAT-Walk uses a novel adaptive and permutation invariant pooling strategy, SetMixer, along with a set-based anonymization process that hides the identity of hyperedges. Finally, we present a simple yet effective neural network model to encode hyperedges. Our evaluation on 10 hypergraph benchmark datasets shows that CAT-Walk attains outstanding performance on temporal hyperedge prediction benchmarks in both inductive and transductive settings. It also shows competitive performance with state-of-the-art methods for node classification. (https://github.com/ubc-systopia/CATWalk)
In this paper, we study the \textit{graph condensation} problem by compressing the large, complex graph into a concise, synthetic representation that preserves the most essential and discriminative information of structure and features. We seminally propose the concept of Shock Absorber (a type of perturbation) that enhances the robustness and stability of the original graphs against changes in an adversarial training fashion. Concretely, (I) we forcibly match the gradients between pre-selected graph neural networks (GNNs) trained on a synthetic, simplified graph and the original training graph at regularly spaced intervals. (II) Before each update synthetic graph point, a Shock Absorber serves as a gradient attacker to maximize the distance between the synthetic dataset and the original graph by selectively perturbing the parts that are underrepresented or insufficiently informative. We iteratively repeat the above two processes (I and II) in an adversarial training fashion to maintain the highly-informative context without losing correlation with the original dataset. More importantly, our shock absorber and the synthesized graph parallelly share the backward process in a free training manner. Compared to the original adversarial training, it introduces almost no additional time overhead. We validate our framework across 8 datasets (3 graph and 5 node classification datasets) and achieve prominent results: for example, on Cora, Citeseer and Ogbn-Arxiv, we can gain nearly 1.13% to 5.03% improvements compare with SOTA models. Moreover, our algorithm adds only about 0.2% to 2.2% additional time overhead over Flicker, Citeseer and Ogbn-Arxiv. Compared to the general adversarial training, our approach improves time efficiency by nearly 4-fold.
Networks are one of the most valuable data structures for modeling problems in the real world. However, the most recent node embedding strategies have focused on undirected graphs, with limited attention to directed graphs, especially directed heterogeneous graphs. In this study, we first investigated the network properties of directed heterogeneous graphs. Based on network analysis, we proposed an embedding method, a bidirectional heterogeneous graph neural network with random teleport (BHGNN-RT), for directed heterogeneous graphs, that leverages bidirectional message-passing process and network heterogeneity. With the optimization of teleport proportion, BHGNN-RT is beneficial to overcome the over-smoothing problem. Extensive experiments on various datasets were conducted to verify the efficacy and efficiency of BHGNN-RT. Furthermore, we investigated the effects of message components, model layer, and teleport proportion on model performance. The performance comparison with all other baselines illustrates that BHGNN-RT achieves state-of-the-art performance, outperforming the benchmark methods in both node classification and unsupervised clustering tasks.
The latest advancements in large language models (LLMs) have revolutionized the field of natural language processing (NLP). Inspired by the success of LLMs in NLP tasks, some recent work has begun investigating the potential of applying LLMs in graph learning tasks. However, most of the existing work focuses on utilizing LLMs as powerful node feature augmenters, leaving employing LLMs to enhance graph topological structures an understudied problem. In this work, we explore how to leverage the information retrieval and text generation capabilities of LLMs to refine/enhance the topological structure of text-attributed graphs (TAGs) under the node classification setting. First, we propose using LLMs to help remove unreliable edges and add reliable ones in the TAG. Specifically, we first let the LLM output the semantic similarity between node attributes through delicate prompt designs, and then perform edge deletion and edge addition based on the similarity. Second, we propose using pseudo-labels generated by the LLM to improve graph topology, that is, we introduce the pseudo-label propagation as a regularization to guide the graph neural network (GNN) in learning proper edge weights. Finally, we incorporate the two aforementioned LLM-based methods for graph topological refinement into the process of GNN training, and perform extensive experiments on four real-world datasets. The experimental results demonstrate the effectiveness of LLM-based graph topology refinement (achieving a 0.15%--2.47% performance gain on public benchmarks).
While graph neural networks have achieved state-of-the-art performances in many real-world tasks including graph classification and node classification, recent works have demonstrated they are also extremely vulnerable to adversarial attacks. Most previous works have focused on attacking node classification networks under impractical white-box scenarios. In this work, we will propose a non-targeted Hard Label Black Box Node Injection Attack on Graph Neural Networks, which to the best of our knowledge, is the first of its kind. Under this setting, more real world tasks can be studied because our attack assumes no prior knowledge about (1): the model architecture of the GNN we are attacking; (2): the model's gradients; (3): the output logits of the target GNN model. Our attack is based on an existing edge perturbation attack, from which we restrict the optimization process to formulate a node injection attack. In the work, we will evaluate the performance of the attack using three datasets, COIL-DEL, IMDB-BINARY, and NCI1.
We propose a method for the classification of objects that are structured as random trees. Our aim is to model a distribution over the node label assignments in settings where the tree data structure is associated with node attributes (typically high dimensional embeddings). The tree topology is not predetermined and none of the label assignments are present during inference. Other methods that produce a distribution over node label assignment in trees (or more generally in graphs) either assume conditional independence of the label assignment, operate on a fixed graph topology, or require part of the node labels to be observed. Our method defines a Markov Network with the corresponding topology of the random tree and an associated Gibbs distribution. We parameterize the Gibbs distribution with a Graph Neural Network that operates on the random tree and the node embeddings. This allows us to estimate the likelihood of node assignments for a given random tree and use MCMC to sample from the distribution of node assignments. We evaluate our method on the tasks of node classification in trees on the Stanford Sentiment Treebank dataset. Our method outperforms the baselines on this dataset, demonstrating its effectiveness for modeling joint distributions of node labels in random trees.
Recently, pretraining methods for the Graph Neural Networks (GNNs) have been successful at learning effective representations from unlabeled graph data. However, most of these methods rely on pairwise relations in the graph and do not capture the underling higher-order relations between entities. Hypergraphs are versatile and expressive structures that can effectively model higher-order relationships among entities in the data. Despite the efforts to adapt GNNs to hypergraphs (HyperGNN), there are currently no fully self-supervised pretraining methods for HyperGNN on heterogeneous hypergraphs. In this paper, we present SPHH, a novel self-supervised pretraining framework for heterogeneous HyperGNNs. Our method is able to effectively capture higher-order relations among entities in the data in a self-supervised manner. SPHH is consist of two self-supervised pretraining tasks that aim to simultaneously learn both local and global representations of the entities in the hypergraph by using informative representations derived from the hypergraph structure. Overall, our work presents a significant advancement in the field of self-supervised pretraining of HyperGNNs, and has the potential to improve the performance of various graph-based downstream tasks such as node classification and link prediction tasks which are mapped to hypergraph configuration. Our experiments on two real-world benchmarks using four different HyperGNN models show that our proposed SPHH framework consistently outperforms state-of-the-art baselines in various downstream tasks. The results demonstrate that SPHH is able to improve the performance of various HyperGNN models in various downstream tasks, regardless of their architecture or complexity, which highlights the robustness of our framework.
Recent studies attempted to utilize multilayer perceptrons (MLPs) to solve semi-supervised node classification on graphs, by training a student MLP by knowledge distillation (KD) from a teacher graph neural network (GNN). While previous studies have focused mostly on training the student MLP by matching the output probability distributions between the teacher and student models during KD, it has not been systematically studied how to inject the structural information in an explicit and interpretable manner. Inspired by GNNs that separate feature transformation $T$ and propagation $\Pi$, we re-frame the KD process as enabling the student MLP to explicitly learn both $T$ and $\Pi$. Although this can be achieved by applying the inverse propagation $\Pi^{-1}$ before distillation from the teacher GNN, it still comes with a high computational cost from large matrix multiplications during training. To solve this problem, we propose Propagate & Distill (P&D), which propagates the output of the teacher GNN before KD and can be interpreted as an approximate process of the inverse propagation $\Pi^{-1}$. Through comprehensive evaluations using real-world benchmark datasets, we demonstrate the effectiveness of P&D by showing further performance boost of the student MLP.
Graph convolutions have been a pivotal element in learning graph representations. However, recursively aggregating neighboring information with graph convolutions leads to indistinguishable node features in deep layers, which is known as the over-smoothing issue. The performance of graph neural networks decays fast as the number of stacked layers increases, and the Dirichlet energy associated with the graph decreases to zero as well. In this work, we introduce a framelet system into the analysis of Dirichlet energy and take a multi-scale perspective to leverage the Dirichlet energy and alleviate the over-smoothing issue. Specifically, we develop a Framelet Augmentation strategy by adjusting the update rules with positive and negative increments for low-pass and high-passes respectively. Based on that, we design the Energy Enhanced Convolution (EEConv), which is an effective and practical operation that is proved to strictly enhance Dirichlet energy. From a message-passing perspective, EEConv inherits multi-hop aggregation property from the framelet transform and takes into account all hops in the multi-scale representation, which benefits the node classification tasks over heterophilous graphs. Experiments show that deep GNNs with EEConv achieve state-of-the-art performance over various node classification datasets, especially for heterophilous graphs, while also lifting the Dirichlet energy as the network goes deeper.
Deep neural networks have achieved significant success in the last decades, but they are not well-calibrated and often produce unreliable predictions. A large number of literature relies on uncertainty quantification to evaluate the reliability of a learning model, which is particularly important for applications of out-of-distribution (OOD) detection and misclassification detection. We are interested in uncertainty quantification for interdependent node-level classification. We start our analysis based on graph posterior networks (GPNs) that optimize the uncertainty cross-entropy (UCE)-based loss function. We describe the theoretical limitations of the widely-used UCE loss. To alleviate the identified drawbacks, we propose a distance-based regularization that encourages clustered OOD nodes to remain clustered in the latent space. We conduct extensive comparison experiments on eight standard datasets and demonstrate that the proposed regularization outperforms the state-of-the-art in both OOD detection and misclassification detection.
Realistic graphs contain both (1) rich self-features of nodes and (2) informative structures of neighborhoods, jointly handled by a Graph Neural Network (GNN) in the typical setup. We propose to decouple the two modalities by Mixture of weak and strong experts (Mowst), where the weak expert is a light-weight Multi-layer Perceptron (MLP), and the strong expert is an off-the-shelf GNN. To adapt the experts' collaboration to different target nodes, we propose a "confidence" mechanism based on the dispersion of the weak expert's prediction logits. The strong expert is conditionally activated in the low-confidence region when either the node's classification relies on neighborhood information, or the weak expert has low model quality. We reveal interesting training dynamics by analyzing the influence of the confidence function on loss: our training algorithm encourages the specialization of each expert by effectively generating soft splitting of the graph. In addition, our "confidence" design imposes a desirable bias toward the strong expert to benefit from GNN's better generalization capability. Mowst is easy to optimize and achieves strong expressive power, with a computation cost comparable to a single GNN. Empirically, Mowst on 4 backbone GNN architectures show significant accuracy improvement on 6 standard node classification benchmarks, including both homophilous and heterophilous graphs (https://github.com/facebookresearch/mowst-gnn).
This paper shows how information about the network's community structure can be used to define node features with high predictive power for classification tasks. To do so, we define a family of community-aware node features and investigate their properties. Those features are designed to ensure that they can be efficiently computed even for large graphs. We show that community-aware node features contain information that cannot be completely recovered by classical node features or node embeddings (both classical and structural) and bring value in node classification tasks. This is verified for various classification tasks on synthetic and real-life networks.
Despite the success of graph neural network models in node classification, edge prediction (the task of predicting missing or potential links between nodes in a graph) remains a challenging problem for these models. A common approach for edge prediction is to first obtain the embeddings of two nodes, and then a predefined scoring function is used to predict the existence of an edge between the two nodes. Here, we introduce a preliminary idea called Edge2Node which suggests to directly obtain an embedding for each edge, without the need for a scoring function. This idea wants to create a new graph H based on the graph G given for the edge prediction task, and then suggests reducing the edge prediction task on G to a node classification task on H. We anticipate that this introductory method could stimulate further investigations for edge prediction task.
Graph research, the systematic study of interconnected data points represented as graphs, plays a vital role in capturing intricate relationships within networked systems. However, in the real world, as graphs scale up, concerns about data security among different data-owning agencies arise, hindering information sharing and, ultimately, the utilization of graph data. Therefore, establishing a mutual trust mechanism among graph agencies is crucial for unlocking the full potential of graphs. Here, we introduce a Cooperative Network Learning (CNL) framework to ensure secure graph computing for various graph tasks. Essentially, this CNL framework unifies the local and global perspectives of GNN computing with distributed data for an agency by virtually connecting all participating agencies as a global graph without a fixed central coordinator. Inter-agency computing is protected by various technologies inherent in our framework, including homomorphic encryption and secure transmission. Moreover, each agency has a fair right to design or employ various graph learning models from its local or global perspective. Thus, CNL can collaboratively train GNN models based on decentralized graphs inferred from local and global graphs. Experiments on contagion dynamics prediction and traditional graph tasks (i.e., node classification and link prediction) demonstrate that our CNL architecture outperforms state-of-the-art GNNs developed at individual sites, revealing that CNL can provide a reliable, fair, secure, privacy-preserving, and global perspective to build effective and personalized models for network applications. We hope this framework will address privacy concerns in graph-related research and integrate decentralized graph data structures to benefit the network research community in cooperation and innovation.
Class imbalance in graph data presents significant challenges for node classification. While existing methods, such as SMOTE-based approaches, partially mitigate this issue, they still exhibit limitations in constructing imbalanced graphs. Generative self-supervised learning (SSL) methods, exemplified by graph autoencoders (GAEs), offer a promising solution by directly generating minority nodes from the data itself, yet their potential remains underexplored. In this paper, we delve into the shortcomings of SMOTE-based approaches in the construction of imbalanced graphs. Furthermore, we introduce VIGraph, a simple yet effective generative SSL approach that relies on the Variational GAE as the fundamental model. VIGraph strictly adheres to the concept of imbalance when constructing imbalanced graphs and innovatively leverages the variational inference (VI) ability of Variational GAE to generate nodes for minority classes. VIGraph introduces comprehensive training strategies, including cross-view contrastive learning at the decoding phase to capture semantic knowledge, adjacency matrix reconstruction to preserve graph structure, and alignment strategy to ensure stable training. VIGraph can generate high-quality nodes directly usable for classification, eliminating the need to integrate the generated nodes back to the graph as well as additional retraining found in SMOTE-based methods. We conduct extensive experiments, results from which demonstrate the superiority and generality of our approach.
The progress in hyperbolic neural networks (HNNs) research is hindered by their absence of inductive bias mechanisms, which are essential for generalizing to new tasks and facilitating scalable learning over large datasets. In this paper, we aim to alleviate these issues by learning generalizable inductive biases from the nodes' local subgraph and transfer them for faster learning over new subgraphs with a disjoint set of nodes, edges, and labels in a few-shot setting. We introduce a novel method, Hyperbolic GRAph Meta Learner (H-GRAM), that, for the tasks of node classification and link prediction, learns transferable information from a set of support local subgraphs in the form of hyperbolic meta gradients and label hyperbolic protonets to enable faster learning over a query set of new tasks dealing with disjoint subgraphs. Furthermore, we show that an extension of our meta-learning framework also mitigates the scalability challenges seen in HNNs faced by existing approaches. Our comparative analysis shows that H-GRAM effectively learns and transfers information in multiple challenging few-shot settings compared to other state-of-the-art baselines. Additionally, we demonstrate that, unlike standard HNNs, our approach is able to scale over large graph datasets and improve performance over its Euclidean counterparts.
Graph Neural Networks (GNNs) are powerful in learning semantics of graph data. Recently, a new paradigm "pre-train and prompt" has shown promising results in adapting GNNs to various tasks with less supervised data. The success of such paradigm can be attributed to the more consistent objectives of pre-training and task-oriented prompt tuning, where the pre-trained knowledge can be effectively transferred to downstream tasks. Most existing methods are based on the class prototype vector framework. However, in the few-shot scenarios, given few labeled data, class prototype vectors are difficult to be accurately constructed or learned. Meanwhile, the structure information of graph is usually exploited during pre-training for learning node representations, while neglected in the prompt tuning stage for learning more accurate prototype vectors. In addition, they generally ignore the impact of heterophilous neighborhoods on node representation and are not suitable for heterophilous graphs. To bridge these gaps, we propose a novel pre-training and structure prompt tuning framework for GNNs, namely PSP, which consistently exploits structure information in both pre-training and prompt tuning stages. In particular, PSP 1) employs a dual-view contrastive learning to align the latent semantic spaces of node attributes and graph structure, and 2) incorporates structure information in prompted graph to construct more accurate prototype vectors and elicit more pre-trained knowledge in prompt tuning. We conduct extensive experiments on node classification and graph classification tasks to evaluate the effectiveness of PSP. We show that PSP can lead to superior performance in few-shot scenarios on both homophilous and heterophilous graphs. The implemented code is available at https://github.com/gqq1210/PSP.
Graph neural networks (GNNs) have emerged as a powerful tool for tasks such as node classification and graph classification. However, much less work has been done on signal classification, where the data consists of many functions (referred to as signals) defined on the vertices of a single graph. These tasks require networks designed differently from those designed for traditional GNN tasks. Indeed, traditional GNNs rely on localized low-pass filters, and signals of interest may have intricate multi-frequency behavior and exhibit long range interactions. This motivates us to introduce the BLIS-Net (Bi-Lipschitz Scattering Net), a novel GNN that builds on the previously introduced geometric scattering transform. Our network is able to capture both local and global signal structure and is able to capture both low-frequency and high-frequency information. We make several crucial changes to the original geometric scattering architecture which we prove increase the ability of our network to capture information about the input signal and show that BLIS-Net achieves superior performance on both synthetic and real-world data sets based on traffic flow and fMRI data.