Graph representation learning methods are highly effective in handling complex non-Euclidean data by capturing intricate relationships and features within graph structures. However, traditional methods face challenges when dealing with heterogeneous graphs that contain various types of nodes and edges due to the diverse sources and complex nature of the data. Existing Heterogeneous Graph Neural Networks (HGNNs) have shown promising results but require prior knowledge of node and edge types and unified node feature formats, which limits their applicability. Recent advancements in graph representation learning using Large Language Models (LLMs) offer new solutions by integrating LLMs' data processing capabilities, enabling the alignment of various graph representations. Nevertheless, these methods often overlook heterogeneous graph data and require extensive preprocessing. To address these limitations, we propose a novel method that leverages the strengths of both LLM and GNN, allowing for the processing of graph data with any format and type of nodes and edges without the need for type information or special preprocessing. Our method employs LLM to automatically summarize and classify different data formats and types, aligns node features, and uses a specialized GNN for targeted learning, thus obtaining effective graph representations for downstream tasks. Theoretical analysis and experimental validation have demonstrated the effectiveness of our method.
AI becomes increasingly vital for telecom industry, as the burgeoning complexity of upcoming mobile communication networks places immense pressure on network operators. While there is a growing consensus that intelligent network self-driving holds the key, it heavily relies on expert experience and knowledge extracted from network data. In an effort to facilitate convenient analytics and utilization of wireless big data, we introduce the concept of knowledge graphs into the field of mobile networks, giving rise to what we term as wireless data knowledge graphs (WDKGs). However, the heterogeneous and dynamic nature of communication networks renders manual WDKG construction both prohibitively costly and error-prone, presenting a fundamental challenge. In this context, we propose an unsupervised data-and-model driven graph structure learning (DMGSL) framework, aimed at automating WDKG refinement and updating. Tackling WDKG heterogeneity involves stratifying the network into homogeneous layers and refining it at a finer granularity. Furthermore, to capture WDKG dynamics effectively, we segment the network into static snapshots based on the coherence time and harness the power of recurrent neural networks to incorporate historical information. Extensive experiments conducted on the established WDKG demonstrate the superiority of the DMGSL over the baselines, particularly in terms of node classification accuracy.
Software vendors often silently release security patches without providing sufficient advisories (e.g., Common Vulnerabilities and Exposures) or delayed updates via resources (e.g., National Vulnerability Database). Therefore, it has become crucial to detect these security patches to ensure secure software maintenance. However, existing methods face the following challenges: (1) They primarily focus on the information within the patches themselves, overlooking the complex dependencies in the repository. (2) Security patches typically involve multiple functions and files, increasing the difficulty in well learning the representations. To alleviate the above challenges, this paper proposes a Repository-level Security Patch Detection framework named RepoSPD, which comprises three key components: 1) a repository-level graph construction, RepoCPG, which represents software patches by merging pre-patch and post-patch source code at the repository level; 2) a structure-aware patch representation, which fuses the graph and sequence branch and aims at comprehending the relationship among multiple code changes; 3) progressive learning, which facilitates the model in balancing semantic and structural information. To evaluate RepoSPD, we employ two widely-used datasets in security patch detection: SPI-DB and PatchDB. We further extend these datasets to the repository level, incorporating a total of 20,238 and 28,781 versions of repository in C/C++ programming languages, respectively, denoted as SPI-DB* and PatchDB*. We compare RepoSPD with six existing security patch detection methods and five static tools. Our experimental results demonstrate that RepoSPD outperforms the state-of-the-art baseline, with improvements of 11.90%, and 3.10% in terms of accuracy on the two datasets, respectively.
Graph neural networks (GNNs) are powerful machine learning models designed to handle irregularly structured data. However, their generic design often proves inadequate for analyzing brain connectomes in Alzheimer's Disease (AD), highlighting the need to incorporate domain knowledge for optimal performance. Infusing AD-related knowledge into GNNs is a complicated task. Existing methods typically rely on collaboration between computer scientists and domain experts, which can be both time-intensive and resource-demanding. To address these limitations, this paper presents a novel self-guided, knowledge-infused multimodal GNN that autonomously incorporates domain knowledge into the model development process. Our approach conceptualizes domain knowledge as natural language and introduces a specialized multimodal GNN capable of leveraging this uncurated knowledge to guide the learning process of the GNN, such that it can improve the model performance and strengthen the interpretability of the predictions. To evaluate our framework, we curated a comprehensive dataset of recent peer-reviewed papers on AD and integrated it with multiple real-world AD datasets. Experimental results demonstrate the ability of our method to extract relevant domain knowledge, provide graph-based explanations for AD diagnosis, and improve the overall performance of the GNN. This approach provides a more scalable and efficient alternative to inject domain knowledge for AD compared with the manual design from the domain expert, advancing both prediction accuracy and interpretability in AD diagnosis.
Graphs are ubiquitous in real-world applications, ranging from social networks to biological systems, and have inspired the development of Graph Neural Networks (GNNs) for learning expressive representations. While most research has centered on static graphs, many real-world scenarios involve dynamic, temporally evolving graphs, motivating the need for Continuous-Time Dynamic Graph (CTDG) models. This paper provides a comprehensive review of Graph Representation Learning (GRL) on CTDGs with a focus on Self-Supervised Representation Learning (SSRL). We introduce a novel theoretical framework that analyzes the expressivity of CTDG models through an Information-Flow (IF) lens, quantifying their ability to propagate and encode temporal and structural information. Leveraging this framework, we categorize existing CTDG methods based on their suitability for different graph types and application scenarios. Within the same scope, we examine the design of SSRL methods tailored to CTDGs, such as predictive and contrastive approaches, highlighting their potential to mitigate the reliance on labeled data. Empirical evaluations on synthetic and real-world datasets validate our theoretical insights, demonstrating the strengths and limitations of various methods across long-range, bi-partite and community-based graphs. This work offers both a theoretical foundation and practical guidance for selecting and developing CTDG models, advancing the understanding of GRL in dynamic settings.
Graph Neural Networks (GNNs) have demonstrated strong performance in graph representation learning across various real-world applications. However, they often produce biased predictions caused by sensitive attributes, such as religion or gender, an issue that has been largely overlooked in existing methods. Recently, numerous studies have focused on reducing biases in GNNs. However, these approaches often rely on training with partial data (e.g., using either node features or graph structure alone), which can enhance fairness but frequently compromises model utility due to the limited utilization of available graph information. To address this tradeoff, we propose an effective strategy to balance fairness and utility in knowledge distillation. Specifically, we introduce FairDTD, a novel Fair representation learning framework built on Dual-Teacher Distillation, leveraging a causal graph model to guide and optimize the design of the distillation process. Specifically, FairDTD employs two fairness-oriented teacher models: a feature teacher and a structure teacher, to facilitate dual distillation, with the student model learning fairness knowledge from the teachers while also leveraging full data to mitigate utility loss. To enhance information transfer, we incorporate graph-level distillation to provide an indirect supplement of graph information during training, as well as a node-specific temperature module to improve the comprehensive transfer of fair knowledge. Experiments on diverse benchmark datasets demonstrate that FairDTD achieves optimal fairness while preserving high model utility, showcasing its effectiveness in fair representation learning for GNNs.
Recent advancements in Spectral Graph Convolutional Networks (SpecGCNs) have led to state-of-the-art performance in various graph representation learning tasks. To exploit the potential of SpecGCNs, we analyze corresponding graph filters via polynomial interpolation, the cornerstone of graph signal processing. Different polynomial bases, such as Bernstein, Chebyshev, and monomial basis, have various convergence rates that will affect the error in polynomial interpolation. Although adopting Chebyshev basis for interpolation can minimize maximum error, the performance of ChebNet is still weaker than GPR-GNN and BernNet. \textbf{We point out it is caused by the Gibbs phenomenon, which occurs when the graph frequency response function approximates the target function.} It reduces the approximation ability of a truncated polynomial interpolation. In order to mitigate the Gibbs phenomenon, we propose to add the Gibbs damping factor with each term of Chebyshev polynomials on ChebNet. As a result, our lightweight approach leads to a significant performance boost. Afterwards, we reorganize ChebNet via decoupling feature propagation and transformation. We name this variant as \textbf{ChebGibbsNet}. Our experiments indicate that ChebGibbsNet is superior to other advanced SpecGCNs, such as GPR-GNN and BernNet, in both homogeneous graphs and heterogeneous graphs.
Graph Transformers (GTs) have demonstrated significant advantages in graph representation learning through their global attention mechanisms. However, the self-attention mechanism in GTs tends to neglect the inductive biases inherent in graph structures, making it chanllenging to effectively capture essential structural information. To address this issue, we propose a novel approach that integrate graph inductive bias into self-attention mechanisms by leveraging quantum technology for structural encoding. In this paper, we introduce the Graph Quantum Walk Transformer (GQWformer), a groundbreaking GNN framework that utilizes quantum walks on attributed graphs to generate node quantum states. These quantum states encapsulate rich structural attributes and serve as inductive biases for the transformer, thereby enabling the generation of more meaningful attention scores. By subsequently incorporating a recurrent neural network, our design amplifies the model's ability to focus on both local and global information. We conducted comprehensive experiments across five publicly available datasets to evaluate the effectiveness of our model. These results clearly indicate that GQWformer outperforms existing state-of-the-art graph classification algorithms. These findings highlight the significant potential of integrating quantum computing methodologies with traditional GNNs to advance the field of graph representation learning, providing a promising direction for future research and applications.
In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.
Graph neural networks stand as the predominant technique for graph representation learning owing to their strong expressive power, yet the performance highly depends on the availability of high-quality labels in an end-to-end manner. Thus the pretraining and fine-tuning paradigm has been proposed to mitigate the label cost issue. Subsequently, the gap between the pretext tasks and downstream tasks has spurred the development of graph prompt learning which inserts a set of graph prompts into the original graph data with minimal parameters while preserving competitive performance. However, the current exploratory works are still limited since they all concentrate on learning fixed task-specific prompts which may not generalize well across the diverse instances that the task comprises. To tackle this challenge, we introduce Instance-Aware Graph Prompt Learning (IA-GPL) in this paper, aiming to generate distinct prompts tailored to different input instances. The process involves generating intermediate prompts for each instance using a lightweight architecture, quantizing these prompts through trainable codebook vectors, and employing the exponential moving average technique to ensure stable training. Extensive experiments conducted on multiple datasets and settings showcase the superior performance of IA-GPL compared to state-of-the-art baselines.
Graph Transformers (GTs) have demonstrated remarkable performance in incorporating various graph structure information, e.g., long-range structural dependency, into graph representation learning. However, self-attention -- the core module of GTs -- preserves only low-frequency signals on graph features, retaining only homophilic patterns that capture similar features among the connected nodes. Consequently, it has insufficient capacity in modeling complex node label patterns, such as the opposite of homophilic patterns -- heterophilic patterns. Some improved GTs deal with the problem by learning polynomial filters or performing self-attention over the first-order graph spectrum. However, these GTs either ignore rich information contained in the whole spectrum or neglect higher-order spectrum information, resulting in limited flexibility and frequency response in their spectral filters. To tackle these challenges, we propose a novel GT network, namely Graph Fourier Kolmogorov-Arnold Transformers (GrokFormer), to go beyond the self-attention in GTs. GrokFormer leverages learnable activation functions in order-$K$ graph spectrum through Fourier series modeling to i) learn eigenvalue-targeted filter functions producing learnable base that can capture a broad range of frequency signals flexibly, and ii) extract first- and higher-order graph spectral information adaptively. In doing so, GrokFormer can effectively capture intricate patterns hidden across different orders and levels of frequency signals, learning expressive, order-and-frequency-adaptive graph representations. Comprehensive experiments conducted on 10 node classification datasets across various domains, scales, and levels of graph heterophily, as well as 5 graph classification datasets, demonstrate that GrokFormer outperforms state-of-the-art GTs and other advanced graph neural networks.
Leveraging the diversity and quantity of data provided by various graph-structured data augmentations while preserving intrinsic semantic information is challenging. Additionally, successive layers in graph neural network (GNN) tend to produce more similar node embeddings, while graph contrastive learning aims to increase the dissimilarity between negative pairs of node embeddings. This inevitably results in a conflict between the message-passing mechanism (MPM) of GNNs and the contrastive learning (CL) of negative pairs via intraviews. In this paper, we propose a conditional distribution learning (CDL) method that learns graph representations from graph-structured data for semisupervised graph classification. Specifically, we present an end-to-end graph representation learning model to align the conditional distributions of weakly and strongly augmented features over the original features. This alignment enables the CDL model to effectively preserve intrinsic semantic information when both weak and strong augmentations are applied to graph-structured data. To avoid the conflict between the MPM and the CL of negative pairs, positive pairs of node representations are retained for measuring the similarity between the original features and the corresponding weakly augmented features. Extensive experiments with several benchmark graph datasets demonstrate the effectiveness of the proposed CDL method.
In the field of deep learning, Graph Neural Networks (GNNs) and Graph Transformer models, with their outstanding performance and flexible architectural designs, have become leading technologies for processing structured data, especially graph data. Traditional GNNs often face challenges in capturing information from distant vertices effectively. In contrast, Graph Transformer models are particularly adept at managing long-distance node relationships. Despite these advantages, Graph Transformer models still encounter issues with computational and storage efficiency when scaled to large graph datasets. To address these challenges, we propose an innovative Graph Neural Network (GNN) architecture that integrates a Top-m attention mechanism aggregation component and a neighborhood aggregation component, effectively enhancing the model's ability to aggregate relevant information from both local and extended neighborhoods at each layer. This method not only improves computational efficiency but also enriches the node features, facilitating a deeper analysis of complex graph structures. Additionally, to assess the effectiveness of our proposed model, we have applied it to citation sentiment prediction, a novel task previously unexplored in the GNN field. Accordingly, we constructed a dedicated citation network, ArXivNet. In this dataset, we specifically annotated the sentiment polarity of the citations (positive, neutral, negative) to enable in-depth sentiment analysis. Our approach has shown superior performance across a variety of tasks including vertex classification, link prediction, sentiment prediction, graph regression, and visualization. It outperforms existing methods in terms of effectiveness, as demonstrated by experimental results on multiple datasets.
This comprehensive review delves deeply into the various methodologies applied to facial expression recognition (FER) through the lens of graph representation learning (GRL). Initially, we introduce the task of FER and the concepts of graph representation and GRL. Afterward, we discuss some of the most prevalent and valuable databases for this task. We explore promising approaches for graph representation in FER, including graph diffusion, spatio-temporal graphs, and multi-stream architectures. Finally, we identify future research opportunities and provide concluding remarks.
Graphs serve as fundamental descriptors for systems composed of interacting elements, capturing a wide array of data types, from molecular interactions to social networks and knowledge graphs. In this paper, we present an exhaustive review of the latest advancements in graph representation learning and Graph Neural Networks (GNNs). GNNs, tailored to handle graph-structured data, excel in deriving insights and predictions from intricate relational information, making them invaluable for tasks involving such data. Graph representation learning, a pivotal approach in analyzing graph-structured data, facilitates numerous downstream tasks and applications across machine learning, data mining, biomedicine, and healthcare. Our work delves into the capabilities of GNNs, examining their foundational designs and their application in addressing real-world challenges. We introduce a GNN equipped with an advanced high-order pooling function, adept at capturing complex node interactions within graph-structured data. This pooling function significantly enhances the GNN's efficacy in both node- and graph-level tasks. Additionally, we propose a molecular graph generative model with a GNN as its core framework. This GNN backbone is proficient in learning invariant and equivariant molecular characteristics. Employing these features, the molecular graph generative model is capable of simultaneously learning and generating molecular graphs with atom-bond structures and precise atom positions. Our models undergo thorough experimental evaluations and comparisons with established methods, showcasing their superior performance in addressing diverse real-world challenges with various datasets.
Recent papers in the graph machine learning literature have introduced a number of approaches for hyperbolic representation learning. The asserted benefits are improved performance on a variety of graph tasks, node classification and link prediction included. Claims have also been made about the geometric suitability of particular hierarchical graph datasets to representation in hyperbolic space. Despite these claims, our work makes a surprising discovery: when simple Euclidean models with comparable numbers of parameters are properly trained in the same environment, in most cases, they perform as well, if not better, than all introduced hyperbolic graph representation learning models, even on graph datasets previously claimed to be the most hyperbolic as measured by Gromov $\delta$-hyperbolicity (i.e., perfect trees). This observation gives rise to a simple question: how can this be? We answer this question by taking a careful look at the field of hyperbolic graph representation learning as it stands today, and find that a number of papers fail to diligently present baselines, make faulty modelling assumptions when constructing algorithms, and use misleading metrics to quantify geometry of graph datasets. We take a closer look at each of these three problems, elucidate the issues, perform an analysis of methods, and introduce a parametric family of benchmark datasets to ascertain the applicability of (hyperbolic) graph neural networks.
The rapid expansion of Internet of Things (IoT) has resulted in vast, heterogeneous graphs that capture complex interactions among devices, sensors, and systems. Efficient analysis of these graphs is critical for deriving insights in IoT scenarios such as smart cities, industrial IoT, and intelligent transportation systems. However, the scale and diversity of IoT-generated data present significant challenges, and existing methods often struggle with preserving the structural integrity and semantic richness of these complex graphs. Many current approaches fail to maintain the balance between computational efficiency and the quality of the insights generated, leading to potential loss of critical information necessary for accurate decision-making in IoT applications. We introduce HeteroSample, a novel sampling method designed to address these challenges by preserving the structural integrity, node and edge type distributions, and semantic patterns of IoT-related graphs. HeteroSample works by incorporating the novel top-leader selection, balanced neighborhood expansion, and meta-path guided sampling strategies. The key idea is to leverage the inherent heterogeneous structure and semantic relationships encoded by meta-paths to guide the sampling process. This approach ensures that the resulting subgraphs are representative of the original data while significantly reducing computational overhead. Extensive experiments demonstrate that HeteroSample outperforms state-of-the-art methods, achieving up to 15% higher F1 scores in tasks such as link prediction and node classification, while reducing runtime by 20%.These advantages make HeteroSample a transformative tool for scalable and accurate IoT applications, enabling more effective and efficient analysis of complex IoT systems, ultimately driving advancements in smart cities, industrial IoT, and beyond.
Incremental graph learning has gained significant attention for its ability to address the catastrophic forgetting problem in graph representation learning. However, traditional methods often rely on a large number of labels for node classification, which is impractical in real-world applications. This makes few-shot incremental learning on graphs a pressing need. Current methods typically require extensive training samples from meta-learning to build memory and perform intensive fine-tuning of GNN parameters, leading to high memory consumption and potential loss of previously learned knowledge. To tackle these challenges, we introduce Mecoin, an efficient method for building and maintaining memory. Mecoin employs Structured Memory Units to cache prototypes of learned categories, as well as Memory Construction Modules to update these prototypes for new categories through interactions between the nodes and the cached prototypes. Additionally, we have designed a Memory Representation Adaptation Module to store probabilities associated with each class prototype, reducing the need for parameter fine-tuning and lowering the forgetting rate. When a sample matches its corresponding class prototype, the relevant probabilities are retrieved from the MRaM. Knowledge is then distilled back into the GNN through a Graph Knowledge Distillation Module, preserving the model's memory. We analyze the effectiveness of Mecoin in terms of generalization error and explore the impact of different distillation strategies on model performance through experiments and VC-dimension analysis. Compared to other related works, Mecoin shows superior performance in accuracy and forgetting rate. Our code is publicly available on the https://github.com/Arvin0313/Mecoin-GFSCIL.git .
Graph representation learning (GRL) is a fundamental task in machine learning, aiming to encode high-dimensional graph-structured data into low-dimensional vectors. Self-supervised learning (SSL) methods are widely used in GRL because they can avoid expensive human annotation. In this work, we propose a novel Subgraph Gaussian Embedding Contrast (SGEC) method. Our approach introduces a subgraph Gaussian embedding module, which adaptively maps subgraphs to a structured Gaussian space, ensuring the preservation of graph characteristics while controlling the distribution of generated subgraphs. We employ optimal transport distances, including Wasserstein and Gromov-Wasserstein distances, to effectively measure the similarity between subgraphs, enhancing the robustness of the contrastive learning process. Extensive experiments across multiple benchmarks demonstrate that SGEC outperforms or presents competitive performance against state-of-the-art approaches. Our findings provide insights into the design of SSL methods for GRL, emphasizing the importance of the distribution of the generated contrastive pairs.
Graph Neural Networks (GNNs), which are nowadays the benchmark approach in graph representation learning, have been shown to be vulnerable to adversarial attacks, raising concerns about their real-world applicability. While existing defense techniques primarily concentrate on the training phase of GNNs, involving adjustments to message passing architectures or pre-processing methods, there is a noticeable gap in methods focusing on increasing robustness during inference. In this context, this study introduces RobustCRF, a post-hoc approach aiming to enhance the robustness of GNNs at the inference stage. Our proposed method, founded on statistical relational learning using a Conditional Random Field, is model-agnostic and does not require prior knowledge about the underlying model architecture. We validate the efficacy of this approach across various models, leveraging benchmark node classification datasets.