Graph neural networks (GNNs) have emerged as the state of the art for a variety of graph-related tasks and have been widely used in Heterogeneous Graphs (HetGs), where meta-paths help encode specific semantics between various node types. Despite the revolutionary representation capabilities of existing heterogeneous GNNs (HGNNs) due to their focus on improving the effectiveness of heterogeneity capturing, the huge training costs hinder their practical deployment in real-world scenarios that frequently require handling ad-hoc queries with user-defined meta-paths. To address this, we propose FHGE, a Fast Heterogeneous Graph Embedding designed for efficient, retraining-free generation of meta-path-guided graph embeddings. The key design of the proposed framework is two-fold: segmentation and reconstruction modules. It employs Meta-Path Units (MPUs) to segment the graph into local and global components, enabling swift integration of node embeddings from relevant MPUs during reconstruction and allowing quick adaptation to specific meta-paths. In addition, a dual attention mechanism is applied to enhance semantics capturing. Extensive experiments across diverse datasets demonstrate the effectiveness and efficiency of FHGE in generating meta-path-guided graph embeddings and downstream tasks, such as link prediction and node classification, highlighting its significant advantages for real-time graph analysis in ad-hoc queries.
Graph Neural Networks (GNNs) have gained attention for their ability to learn representations from graph data. Due to privacy concerns and conflicts of interest that prevent clients from directly sharing graph data with one another, Vertical Graph Federated Learning (VGFL) frameworks have been developed. Recent studies have shown that VGFL is vulnerable to adversarial attacks that degrade performance. However, it is a common problem that client nodes are often unlabeled in the realm of VGFL. Consequently, the existing attacks, which rely on the availability of labeling information to obtain gradients, are inherently constrained in their applicability. This limitation precludes their deployment in practical, real-world environments. To address the above problems, we propose a novel graph adversarial attack against VGFL, referred to as VGFL-SA, to degrade the performance of VGFL by modifying the local clients structure without using labels. Specifically, VGFL-SA uses a contrastive learning method to complete the attack before the local clients are trained. VGFL-SA first accesses the graph structure and node feature information of the poisoned clients, and generates the contrastive views by node-degree-based edge augmentation and feature shuffling augmentation. Then, VGFL-SA uses the shared graph encoder to get the embedding of each view, and the gradients of the adjacency matrices are obtained by the contrastive function. Finally, perturbed edges are generated using gradient modification rules. We validated the performance of VGFL-SA by performing a node classification task on real-world datasets, and the results show that VGFL-SA achieves good attack effectiveness and transferability.
Recent advancements in Graph Contrastive Learning (GCL) have demonstrated remarkable effectiveness in improving graph representations. However, relying on predefined augmentations (e.g., node dropping, edge perturbation, attribute masking) may result in the loss of task-relevant information and a lack of adaptability to diverse input data. Furthermore, the selection of negative samples remains rarely explored. In this paper, we introduce HyperGCL, a novel multimodal GCL framework from a hypergraph perspective. HyperGCL constructs three distinct hypergraph views by jointly utilizing the input graph's structure and attributes, enabling a comprehensive integration of multiple modalities in contrastive learning. A learnable adaptive topology augmentation technique enhances these views by preserving important relations and filtering out noise. View-specific encoders capture essential characteristics from each view, while a network-aware contrastive loss leverages the underlying topology to define positive and negative samples effectively. Extensive experiments on benchmark datasets demonstrate that HyperGCL achieves state-of-the-art node classification performance.
The application of large language models (LLMs) to graph data has attracted a lot of attention recently. LLMs allow us to use deep contextual embeddings from pretrained models in text-attributed graphs, where shallow embeddings are often used for the text at- tributes of nodes. However, it is still challenging to efficiently en- code the graph structure and features into a sequential form for use by LLMs. In addition, the performance of an LLM alone, is highly dependent on the structure of the input prompt, which limits their effectiveness as a reliable approach and often requires iterative man- ual adjustments that could be slow, tedious and difficult to replicate programmatically. In this paper, we propose GraphiT (Graphs in Text), a framework for encoding graphs into a textual format and optimizing LLM prompts for graph prediction tasks. Here we focus on node classification for text-attributed graphs. We encode the graph data for every node and its neighborhood into a concise text to enable LLMs to better utilize the information in the graph. We then further programmatically optimize the LLM prompts us- ing the DSPy framework to automate this step and make it more efficient and reproducible. GraphiT outperforms our LLM-based baselines on three datasets and we show how the optimization step in GraphiT leads to measurably better results without manual prompt tweaking. We also demonstrated that our graph encoding approach is competitive to other graph encoding methods while being less expensive because it uses significantly less tokens for the same task.
Node tokenized graph Transformers (GTs) have shown promising performance in node classification. The generation of token sequences is the key module in existing tokenized GTs which transforms the input graph into token sequences, facilitating the node representation learning via Transformer. In this paper, we observe that the generations of token sequences in existing GTs only focus on the first-order neighbors on the constructed similarity graphs, which leads to the limited usage of nodes to generate diverse token sequences, further restricting the potential of tokenized GTs for node classification. To this end, we propose a new method termed SwapGT. SwapGT first introduces a novel token swapping operation based on the characteristics of token sequences that fully leverages the semantic relevance of nodes to generate more informative token sequences. Then, SwapGT leverages a Transformer-based backbone to learn node representations from the generated token sequences. Moreover, SwapGT develops a center alignment loss to constrain the representation learning from multiple token sequences, further enhancing the model performance. Extensive empirical results on various datasets showcase the superiority of SwapGT for node classification.
Graph learning has attracted significant attention due to its widespread real-world applications. Current mainstream approaches rely on text node features and obtain initial node embeddings through shallow embedding learning using GNNs, which shows limitations in capturing deep textual semantics. Recent advances in Large Language Models (LLMs) have demonstrated superior capabilities in understanding text semantics, transforming traditional text feature processing. This paper proposes a novel framework that combines Graph Transformer architecture with LLM-enhanced node features. Specifically, we leverage LLMs to generate rich semantic representations of text nodes, which are then processed by a multi-head self-attention mechanism in the Graph Transformer to capture both local and global graph structural information. Our model utilizes the Transformer's attention mechanism to dynamically aggregate neighborhood information while preserving the semantic richness provided by LLM embeddings. Experimental results demonstrate that the LLM-enhanced node features significantly improve the performance of graph learning models on node classification tasks. This approach shows promising results across multiple graph learning tasks, offering a practical direction for combining graph networks with language models.
Graph Neural Networks (GNNs) have demonstrated remarkable proficiency in modeling data with graph structures, yet recent research reveals their susceptibility to adversarial attacks. Traditional attack methodologies, which rely on manipulating the original graph or adding links to artificially created nodes, often prove impractical in real-world settings. This paper introduces a novel adversarial scenario involving the injection of an isolated subgraph to deceive both the link recommender and the node classifier within a GNN system. Specifically, the link recommender is mislead to propose links between targeted victim nodes and the subgraph, encouraging users to unintentionally establish connections and that would degrade the node classification accuracy, thereby facilitating a successful attack. To address this, we present the LiSA framework, which employs a dual surrogate model and bi-level optimization to simultaneously meet two adversarial objectives. Extensive experiments on real-world datasets demonstrate the effectiveness of our method.
Prompt learning has attracted increasing attention in the graph domain as a means to bridge the gap between pretext and downstream tasks. Existing studies on heterogeneous graph prompting typically use feature prompts to modify node features for specific downstream tasks, which do not concern the structure of heterogeneous graphs. Such a design also overlooks information from the meta-paths, which are core to learning the high-order semantics of the heterogeneous graphs. To address these issues, we propose CLEAR, a Cluster-based prompt LEARNING model on heterogeneous graphs. We present cluster prompts that reformulate downstream tasks as heterogeneous graph reconstruction. In this way, we align the pretext and downstream tasks to share the same training objective. Additionally, our cluster prompts are also injected into the meta-paths such that the prompt learning process incorporates high-order semantic information entailed by the meta-paths. Extensive experiments on downstream tasks confirm the superiority of CLEAR. It consistently outperforms state-of-the-art models, achieving up to 5% improvement on the F1 metric for node classification.
The varying degrees of homophily and heterophily in real-world graphs persistently constrain the universality of graph neural networks (GNNs) for node classification. Adopting a data-centric perspective, this work reveals an inherent preference of different graphs towards distinct message encoding schemes: homophilous graphs favor local propagation, while heterophilous graphs exhibit preference for flexible combinations of propagation and transformation. To address this, we propose GNNMoE, a universal node classification framework based on the Mixture-of-Experts (MoE) mechanism. The framework first constructs diverse message-passing experts through recombination of fine-grained encoding operators, then designs soft and hard gating layers to allocate the most suitable expert networks for each node's representation learning, thereby enhancing both model expressiveness and adaptability to diverse graphs. Furthermore, considering that soft gating might introduce encoding noise in homophilous scenarios, we introduce an entropy constraint to guide sharpening of soft gates, achieving organic integration of weighted combination and Top-K selection. Extensive experiments demonstrate that GNNMoE significantly outperforms mainstream GNNs, heterophilous GNNs, and graph transformers in both node classification performance and universality across diverse graph datasets.
Message-passing Graph Neural Networks (GNNs) are often criticized for their limited expressiveness, issues like over-smoothing and over-squashing, and challenges in capturing long-range dependencies, while Graph Transformers (GTs) are considered superior due to their global attention mechanisms. Literature frequently suggests that GTs outperform GNNs, particularly in graph-level tasks such as graph classification and regression. In this study, we explore the untapped potential of GNNs through an enhanced framework, GNN+, which integrates six widely used techniques: edge feature integration, normalization, dropout, residual connections, feed-forward networks, and positional encoding, to effectively tackle graph-level tasks. We conduct a systematic evaluation of three classic GNNs, namely GCN, GIN, and GatedGCN, enhanced by the GNN+ framework across 14 well-known graph-level datasets. Our results show that, contrary to the prevailing belief, classic GNNs excel in graph-level tasks, securing top three rankings across all datasets and achieving first place in eight, while also demonstrating greater efficiency than GTs. This highlights the potential of simple GNN architectures, challenging the belief that complex mechanisms in GTs are essential for superior graph-level performance.
Deep neural networks have enabled researchers to create powerful generalized frameworks, such as transformers, that can be used to solve well-studied problems in various application domains, such as text and image. However, such generalized frameworks are not available for solving graph problems. Graph structures are ubiquitous in many applications around us and many graph problems have been widely studied over years. In recent times, there has been a surge in deep neural network based approaches to solve graph problems, with growing availability of graph structured datasets across diverse domains. Nevertheless, existing methods are mostly tailored to solve a specific task and lack the capability to create a generalized model leading to solutions for different downstream tasks. In this work, we propose a novel, resource-efficient framework named \emph{U}nified \emph{G}raph \emph{N}etwork (UGN) by leveraging the feature extraction capability of graph convolutional neural networks (GCN) and 2-dimensional convolutional neural networks (Conv2D). UGN unifies various graph learning tasks, such as link prediction, node classification, community detection, graph-to-graph translation, knowledge graph completion, and more, within a cohesive framework, while exercising minimal task-specific extensions (e.g., formation of supernodes for coarsening massive networks to increase scalability, use of \textit{mean target connectivity matrix} (MTCM) representation for achieving scalability in graph translation task, etc.) to enhance the generalization capability of graph learning and analysis. We test the novel UGN framework for six uncorrelated graph problems, using twelve different datasets. Experimental results show that UGN outperforms the state-of-the-art baselines by a significant margin on ten datasets, while producing comparable results on the remaining dataset.
Graph Neural Networks (GNNs) have emerged as powerful tools for learning representations of graph-structured data. In addition to real-valued GNNs, quaternion GNNs also perform well on tasks on graph-structured data. With the aim of reducing the energy footprint, we reduce the model size while maintaining accuracy comparable to that of the original-sized GNNs. This paper introduces Quaternion Message Passing Neural Networks (QMPNNs), a framework that leverages quaternion space to compute node representations. Our approach offers a generalizable method for incorporating quaternion representations into GNN architectures at one-fourth of the original parameter count. Furthermore, we present a novel perspective on Graph Lottery Tickets, redefining their applicability within the context of GNNs and QMPNNs. We specifically aim to find the initialization lottery from the subnetwork of the GNNs that can achieve comparable performance to the original GNN upon training. Thereby reducing the trainable model parameters even further. To validate the effectiveness of our proposed QMPNN framework and LTH for both GNNs and QMPNNs, we evaluate their performance on real-world datasets across three fundamental graph-based tasks: node classification, link prediction, and graph classification.
Maximizing the spectral gap through graph rewiring has been proposed to enhance the performance of message-passing graph neural networks (GNNs) by addressing over-squashing. However, as we show, minimizing the spectral gap can also improve generalization. To explain this, we analyze how rewiring can benefit GNNs within the context of stochastic block models. Since spectral gap optimization primarily influences community strength, it improves performance when the community structure aligns with node labels. Building on this insight, we propose three distinct rewiring strategies that explicitly target community structure, node labels, and their alignment: (a) community structure-based rewiring (ComMa), a more computationally efficient alternative to spectral gap optimization that achieves similar goals; (b) feature similarity-based rewiring (FeaSt), which focuses on maximizing global homophily; and (c) a hybrid approach (ComFy), which enhances local feature similarity while preserving community structure to optimize label-community alignment. Extensive experiments confirm the effectiveness of these strategies and support our theoretical insights.
Node classification is a fundamental task in graph analysis, with broad applications across various fields. Recent breakthroughs in Large Language Models (LLMs) have enabled LLM-based approaches for this task. Although many studies demonstrate the impressive performance of LLM-based methods, the lack of clear design guidelines may hinder their practical application. In this work, we aim to establish such guidelines through a fair and systematic comparison of these algorithms. As a first step, we developed LLMNodeBed, a comprehensive codebase and testbed for node classification using LLMs. It includes 10 homophilic datasets, 4 heterophilic datasets, 8 LLM-based algorithms, 8 classic baselines, and 3 learning paradigms. Subsequently, we conducted extensive experiments, training and evaluating over 2,700 models, to determine the key settings (e.g., learning paradigms and homophily) and components (e.g., model size and prompt) that affect performance. Our findings uncover 8 insights, e.g., (1) LLM-based methods can significantly outperform traditional methods in a semi-supervised setting, while the advantage is marginal in a supervised setting; (2) Graph Foundation Models can beat open-source LLMs but still fall short of strong LLMs like GPT-4o in a zero-shot setting. We hope that the release of LLMNodeBed, along with our insights, will facilitate reproducible research and inspire future studies in this field. Codes and datasets are released at \href{https://llmnodebed.github.io/}{\texttt{https://llmnodebed.github.io/}}.
Graph representation learning has emerged as a cornerstone for tasks like node classification and link prediction, yet prevailing self-supervised learning (SSL) methods face challenges such as computational inefficiency, reliance on contrastive objectives, and representation collapse. Existing approaches often depend on feature reconstruction, negative sampling, or complex decoders, which introduce training overhead and hinder generalization. Further, current techniques which address such limitations fail to account for the contribution of node embeddings to a certain prediction in the absence of labeled nodes. To address these limitations, we propose a novel joint embedding predictive framework for graph SSL that eliminates contrastive objectives and negative sampling while preserving semantic and structural information. Additionally, we introduce a semantic-aware objective term that incorporates pseudo-labels derived from Gaussian Mixture Models (GMMs), enhancing node discriminability by evaluating latent feature contributions. Extensive experiments demonstrate that our framework outperforms state-of-the-art graph SSL methods across benchmarks, achieving superior performance without contrastive loss or complex decoders. Key innovations include (1) a non-contrastive, view-invariant joint embedding predictive architecture, (2) Leveraging single context and multiple targets relationship between subgraphs, and (3) GMM-based pseudo-label scoring to capture semantic contributions. This work advances graph SSL by offering a computationally efficient, collapse-resistant paradigm that bridges spatial and semantic graph features for downstream tasks. The code for our paper can be found at https://github.com/Deceptrax123/JPEB-GSSL
Graph learning tasks often hinge on identifying key substructure patterns -- such as triadic closures in social networks or benzene rings in molecular graphs -- that underpin downstream performance. However, most existing graph neural networks (GNNs) rely on message passing, which aggregates local neighborhood information iteratively and struggles to explicitly capture such fundamental motifs, like triangles, k-cliques, and rings. This limitation hinders both expressiveness and long-range dependency modeling. In this paper, we introduce the Neural Graph Pattern Machine (GPM), a novel framework that bypasses message passing by learning directly from graph substructures. GPM efficiently extracts, encodes, and prioritizes task-relevant graph patterns, offering greater expressivity and improved ability to capture long-range dependencies. Empirical evaluations across four standard tasks -- node classification, link prediction, graph classification, and graph regression -- demonstrate that GPM outperforms state-of-the-art baselines. Further analysis reveals that GPM exhibits strong out-of-distribution generalization, desirable scalability, and enhanced interpretability. Code and datasets are available at: https://github.com/Zehong-Wang/GPM.
This study focuses on the application of deep geometric models to solve the 3x3x3 Rubik's Cube. We begin by discussing the cube's graph representation and defining distance as the model's optimization objective. The distance approximation task is reformulated as a node classification problem, effectively addressed using Graph Neural Networks (GNNs). After training the model on a random subgraph, the predicted classes are used to construct a heuristic for $A^*$ search. We conclude with experiments comparing our heuristic to that of the DeepCubeA model.
Graph Neural Networks (GNNs) have demonstrated remarkable effectiveness in various graph representation learning tasks. However, most existing GNNs focus primarily on capturing local information through explicit graph convolution, often neglecting global message-passing. This limitation hinders the establishment of a collaborative interaction between global and local information, which is crucial for comprehensively understanding graph data. To address these challenges, we propose a novel framework called Comprehensive Graph Representation Learning (ComGRL). ComGRL integrates local information into global information to derive powerful representations. It achieves this by implicitly smoothing local information through flexible graph contrastive learning, ensuring reliable representations for subsequent global exploration. Then ComGRL transfers the locally derived representations to a multi-head self-attention module, enhancing their discriminative ability by uncovering diverse and rich global correlations. To further optimize local information dynamically under the self-supervision of pseudo-labels, ComGRL employs a triple sampling strategy to construct mixed node pairs and applies reliable Mixup augmentation across attributes and structure for local contrastive learning. This approach broadens the receptive field and facilitates coordination between local and global representation learning, enabling them to reinforce each other. Experimental results across six widely used graph datasets demonstrate that ComGRL achieves excellent performance in node classification tasks. The code could be available at https://github.com/JinluWang1002/ComGRL.
Graph Neural Networks (GNNs) have shown great success in various graph-based learning tasks. However, it often faces the issue of over-smoothing as the model depth increases, which causes all node representations to converge to a single value and become indistinguishable. This issue stems from the inherent limitations of GNNs, which struggle to distinguish the importance of information from different neighborhoods. In this paper, we introduce MbaGCN, a novel graph convolutional architecture that draws inspiration from the Mamba paradigm-originally designed for sequence modeling. MbaGCN presents a new backbone for GNNs, consisting of three key components: the Message Aggregation Layer, the Selective State Space Transition Layer, and the Node State Prediction Layer. These components work in tandem to adaptively aggregate neighborhood information, providing greater flexibility and scalability for deep GNN models. While MbaGCN may not consistently outperform all existing methods on each dataset, it provides a foundational framework that demonstrates the effective integration of the Mamba paradigm into graph representation learning. Through extensive experiments on benchmark datasets, we demonstrate that MbaGCN paves the way for future advancements in graph neural network research.
Graph Neural Networks (GNNs) combine node attributes over a fixed granularity of the local graph structure around a node to predict its label. However, different nodes may relate to a node-level property with a different granularity of its local neighborhood, and using the same level of smoothing for all nodes can be detrimental to their classification. In this work, we challenge the common fact that a single GNN layer can classify all nodes of a graph by training GNNs with a distinct personalized layer for each node. Inspired by metric learning, we propose a novel algorithm, MetSelect1, to select the optimal representation layer to classify each node. In particular, we identify a prototype representation of each class in a transformed GNN layer and then, classify using the layer where the distance is smallest to a class prototype after normalizing with that layer's variance. Results on 10 datasets and 3 different GNNs show that we significantly improve the node classification accuracy of GNNs in a plug-and-play manner. We also find that using variable layers for prediction enables GNNs to be deeper and more robust to poisoning attacks. We hope this work can inspire future works to learn more adaptive and personalized graph representations.