Graph neural networks (GNNs) are widely used for learning node embeddings in graphs, typically adopting a message-passing scheme. This approach, however, leads to the neighbor explosion problem, with exponentially growing computational and memory demands as layers increase. Graph sampling has become the predominant method for scaling GNNs to large graphs, mitigating but not fully solving the issue. Pre-propagation GNNs (PP-GNNs) represent a new class of models that decouple feature propagation from training through pre-processing, addressing neighbor explosion in theory. Yet, their practical advantages and system-level optimizations remain underexplored. This paper provides a comprehensive characterization of PP-GNNs, comparing them with graph-sampling-based methods in training efficiency, scalability, and accuracy. While PP-GNNs achieve comparable accuracy, we identify data loading as the key bottleneck for training efficiency and input expansion as a major scalability challenge. To address these issues, we propose optimized data loading schemes and tailored training methods that improve PP-GNN training throughput by an average of 15$\times$ over the PP-GNN baselines, with speedup of up to 2 orders of magnitude compared to sampling-based GNNs on large graph benchmarks. Our implementation is publicly available at https://github.com/cornell-zhang/preprop-gnn.
Graph Transformers (GTs), which simultaneously integrate message-passing and self-attention mechanisms, have achieved promising empirical results in some graph prediction tasks. Although these approaches show the potential of Transformers in capturing long-range graph topology information, issues concerning the quadratic complexity and high computing energy consumption severely limit the scalability of GTs on large-scale graphs. Recently, as brain-inspired neural networks, Spiking Neural Networks (SNNs), facilitate the development of graph representation learning methods with lower computational and storage overhead through the unique event-driven spiking neurons. Inspired by these characteristics, we propose a linear-time Graph Transformer using Spiking Vector Quantization (GT-SVQ) for node classification. GT-SVQ reconstructs codebooks based on rate coding outputs from spiking neurons, and injects the codebooks into self-attention blocks to aggregate global information in linear complexity. Besides, spiking vector quantization effectively alleviates codebook collapse and the reliance on complex machinery (distance measure, auxiliary loss, etc.) present in previous vector quantization-based graph learning methods. In experiments, we compare GT-SVQ with other state-of-the-art baselines on node classification datasets ranging from small to large. Experimental results show that GT-SVQ has achieved competitive performances on most datasets while maintaining up to 130x faster inference speed compared to other GTs.
Temporal Graph Networks (TGNs) have demonstrated significant success in dynamic graph tasks such as link prediction and node classification. Both tasks comprise transductive settings, where the model predicts links among known nodes, and in inductive settings, where it generalises learned patterns to previously unseen nodes. Existing TGN designs face a dilemma under these dual scenarios. Anonymous TGNs, which rely solely on temporal and structural information, offer strong inductive generalisation but struggle to distinguish known nodes. In contrast, non-anonymous TGNs leverage node features to excel in transductive tasks yet fail to adapt to new nodes. To address this challenge, we propose Trajectory Encoding TGN (TETGN). Our approach introduces automatically expandable node identifiers (IDs) as learnable temporal positional features and performs message passing over these IDs to capture each node's historical context. By integrating this trajectory-aware module with a standard TGN using multi-head attention, TETGN effectively balances transductive accuracy with inductive generalisation. Experimental results on three real-world datasets show that TETGN significantly outperforms strong baselines on both link prediction and node classification tasks, demonstrating its ability to unify the advantages of anonymous and non-anonymous models for dynamic graph learning.
Circuit representation learning has shown promise in advancing Electronic Design Automation (EDA) by capturing structural and functional circuit properties for various tasks. Existing pre-trained solutions rely on graph learning with complex functional supervision, such as truth table simulation. However, they only handle simple and-inverter graphs (AIGs), struggling to fully encode other complex gate functionalities. While large language models (LLMs) excel at functional understanding, they lack the structural awareness for flattened netlists. To advance netlist representation learning, we present NetTAG, a netlist foundation model that fuses gate semantics with graph structure, handling diverse gate types and supporting a variety of functional and physical tasks. Moving beyond existing graph-only methods, NetTAG formulates netlists as text-attributed graphs, with gates annotated by symbolic logic expressions and physical characteristics as text attributes. Its multimodal architecture combines an LLM-based text encoder for gate semantics and a graph transformer for global structure. Pre-trained with gate and graph self-supervised objectives and aligned with RTL and layout stages, NetTAG captures comprehensive circuit intrinsics. Experimental results show that NetTAG consistently outperforms each task-specific method on four largely different functional and physical tasks and surpasses state-of-the-art AIG encoders, demonstrating its versatility.
Dynamic graph learning is essential for applications involving temporal networks and requires effective modeling of temporal relationships. Seminal attention-based models like TGAT and DyGFormer rely on sinusoidal time encoders to capture temporal relationships between edge events. In this paper, we study a simpler alternative: the linear time encoder, which avoids temporal information loss caused by sinusoidal functions and reduces the need for high dimensional time encoders. We show that the self-attention mechanism can effectively learn to compute time spans from linear time encodings and extract relevant temporal patterns. Through extensive experiments on six dynamic graph datasets, we demonstrate that the linear time encoder improves the performance of TGAT and DyGFormer in most cases. Moreover, the linear time encoder can lead to significant savings in model parameters with minimal performance loss. For example, compared to a 100-dimensional sinusoidal time encoder, TGAT with a 2-dimensional linear time encoder saves 43% of parameters and achieves higher average precision on five datasets. These results can be readily used to positively impact the design choices of a wide variety of dynamic graph learning architectures. The experimental code is available at: https://github.com/hsinghuan/dg-linear-time.git.
In graph signal processing, learning the weighted connections between nodes from a set of sample signals is a fundamental task when the underlying relationships are not known a priori. This task is typically addressed by finding a graph Laplacian on which the observed signals are smooth. With the extension of graphs to hypergraphs - where edges can connect more than two nodes - graph learning methods have similarly been generalized to hypergraphs. However, the absence of a unified framework for calculating total variation has led to divergent definitions of smoothness and, consequently, differing approaches to hyperedge recovery. We confront this challenge through generalization of several previously proposed hypergraph total variations, subsequently allowing ease of substitution into a vector based optimization. To this end, we propose a novel hypergraph learning method that recovers a hypergraph topology from time-series signals based on a smoothness prior. Our approach addresses key limitations in prior works, such as hyperedge selection and convergence issues, by formulating the problem as a convex optimization solved via a forward-backward-forward algorithm, ensuring guaranteed convergence. Additionally, we introduce a process that simultaneously limits the span of the hyperedge search and maintains a valid hyperedge selection set. In doing so, our method becomes scalable in increasingly complex network structures. The experimental results demonstrate improved performance, in terms of accuracy, over other state-of-the-art hypergraph inference methods; furthermore, we empirically show our method to be robust to total variation terms, biased towards global smoothness, and scalable to larger hypergraphs.
While graph neural networks (GNNs) operating in hyperbolic spaces have shown promise for modeling hierarchical and complex relational data, a critical limitation often overlooked is their potentially limited discriminative power compared to their Euclidean counterparts or fundamental graph isomorphism tests like the Weisfeiler-Lehman (WL) hierarchy. Existing hyperbolic aggregation schemes, while curvature-aware, may not sufficiently capture the intricate structural differences required to robustly distinguish non-isomorphic graphs owing to non-injective aggregation functions. To address this expressiveness gap in hyperbolic graph learning, we introduce the Lorentzian Graph Isomorphic Network (LGIN), a novel GNN designed to achieve enhanced discriminative capabilities within the Lorentzian model of hyperbolic space. LGIN proposes a new update rule that effectively combines local neighborhood information with a richer representation of graph structure designed to preserve the Lorentzian metric tensor. This represents a significant step towards building more expressive GNNs in non-Euclidean geometries, overcoming a common bottleneck in current hyperbolic methods. We conduct extensive evaluations across nine diverse benchmark datasets, including molecular and protein structures. LGIN consistently outperforms or matches state-of-the-art hyperbolic and Euclidean GNNs, showcasing its practical efficacy and validating its superior ability to capture complex graph structures and distinguish between different graphs. To the best of our knowledge, LGIN is the first work to study the framework behind a powerful GNN on the hyperbolic space. The code for our paper can be found at https://github.com/Deceptrax123/LGIN
Financial institutions are required by regulation to report suspicious financial transactions related to money laundering. Therefore, they need to constantly monitor vast amounts of incoming and outgoing transactions. A particular challenge in detecting money laundering is that money launderers continuously adapt their tactics to evade detection. Hence, detection methods need constant fine-tuning. Traditional machine learning models suffer from catastrophic forgetting when fine-tuning the model on new data, thereby limiting their effectiveness in dynamic environments. Continual learning methods may address this issue and enhance current anti-money laundering (AML) practices, by allowing models to incorporate new information while retaining prior knowledge. Research on continual graph learning for AML, however, is still scarce. In this review, we critically evaluate state-of-the-art continual graph learning approaches for AML applications. We categorise methods into replay-based, regularization-based, and architecture-based strategies within the graph neural network (GNN) framework, and we provide in-depth experimental evaluations on both synthetic and real-world AML data sets that showcase the effect of the different hyperparameters. Our analysis demonstrates that continual learning improves model adaptability and robustness in the face of extreme class imbalances and evolving fraud patterns. Finally, we outline key challenges and propose directions for future research.
The skip-gram model (SGM), which employs a neural network to generate node vectors, serves as the basis for numerous popular graph embedding techniques. However, since the training datasets contain sensitive linkage information, the parameters of a released SGM may encode private information and pose significant privacy risks. Differential privacy (DP) is a rigorous standard for protecting individual privacy in data analysis. Nevertheless, when applying differential privacy to skip-gram in graphs, it becomes highly challenging due to the complex link relationships, which potentially result in high sensitivity and necessitate substantial noise injection. To tackle this challenge, we present AdvSGM, a differentially private skip-gram for graphs via adversarial training. Our core idea is to leverage adversarial training to privatize skip-gram while improving its utility. Towards this end, we develop a novel adversarial training module by devising two optimizable noise terms that correspond to the parameters of a skip-gram. By fine-tuning the weights between modules within AdvSGM, we can achieve differentially private gradient updates without additional noise injection. Extensive experimental results on six real-world graph datasets show that AdvSGM preserves high data utility across different downstream tasks.
Recent advances in graph learning have paved the way for innovative retrieval-augmented generation (RAG) systems that leverage the inherent relational structures in graph data. However, many existing approaches suffer from rigid, fixed settings and significant engineering overhead, limiting their adaptability and scalability. Additionally, the RAG community has largely overlooked the decades of research in the graph database community regarding the efficient retrieval of interesting substructures on large-scale graphs. In this work, we introduce the RAG-on-Graphs Library (RGL), a modular framework that seamlessly integrates the complete RAG pipeline-from efficient graph indexing and dynamic node retrieval to subgraph construction, tokenization, and final generation-into a unified system. RGL addresses key challenges by supporting a variety of graph formats and integrating optimized implementations for essential components, achieving speedups of up to 143x compared to conventional methods. Moreover, its flexible utilities, such as dynamic node filtering, allow for rapid extraction of pertinent subgraphs while reducing token consumption. Our extensive evaluations demonstrate that RGL not only accelerates the prototyping process but also enhances the performance and applicability of graph-based RAG systems across a range of tasks.
Natural products, as metabolites from microorganisms, animals, or plants, exhibit diverse biological activities, making them crucial for drug discovery. Nowadays, existing deep learning methods for natural products research primarily rely on supervised learning approaches designed for specific downstream tasks. However, such one-model-for-a-task paradigm often lacks generalizability and leaves significant room for performance improvement. Additionally, existing molecular characterization methods are not well-suited for the unique tasks associated with natural products. To address these limitations, we have pre-trained a foundation model for natural products based on their unique properties. Our approach employs a novel pretraining strategy that is especially tailored to natural products. By incorporating contrastive learning and masked graph learning objectives, we emphasize evolutional information from molecular scaffolds while capturing side-chain information. Our framework achieves state-of-the-art (SOTA) results in various downstream tasks related to natural product mining and drug discovery. We first compare taxonomy classification with synthesized molecule-focused baselines to demonstrate that current models are inadequate for understanding natural synthesis. Furthermore, by diving into a fine-grained analysis at both the gene and microbial levels, NaFM demonstrates the ability to capture evolutionary information. Eventually, our method is experimented with virtual screening, illustrating informative natural product representations that can lead to more effective identification of potential drug candidates.
Network-wide Traffic State Estimation (TSE), which aims to infer a complete image of network traffic states with sparsely deployed sensors, plays a vital role in intelligent transportation systems. With the development of data-driven methods, traffic dynamics modeling has advanced significantly. However, TSE poses fundamental challenges for data-driven approaches, since historical patterns cannot be learned locally at sensor-free segments. Although inductive graph learning shows promise in estimating states at locations without sensor, existing methods typically handle unobserved locations by filling them with zeros, introducing bias to the sensitive graph message propagation. The recently proposed Dirichlet Energy-based Feature Propagation (DEFP) method achieves State-Of-The-Art (SOTA) performance in unobserved node classification by eliminating the need for zero-filling. However, applying it to TSE faces three key challenges: inability to handle directed traffic networks, strong assumptions in traffic spatial correlation modeling, and overlooks distinct propagation rules of different patterns (e.g., congestion and free flow). We propose DGAE, a novel inductive graph representation model that addresses these challenges through theoretically derived DEFP for Directed graph (DEFP4D), enhanced spatial representation learning via DEFP4D-guided latent space encoding, and physics-guided propagation mechanisms that separately handles congested and free-flow patterns. Experiments on three traffic datasets demonstrate that DGAE outperforms existing SOTA methods and exhibits strong cross-city transferability. Furthermore, DEFP4D can serve as a standalone lightweight solution, showing superior performance under extremely sparse sensor conditions.
Graph Anomaly Detection (GAD) plays a vital role in various data mining applications such as e-commerce fraud prevention and malicious user detection. Recently, Graph Neural Network (GNN) based approach has demonstrated great effectiveness in GAD by first encoding graph data into low-dimensional representations and then identifying anomalies under the guidance of supervised or unsupervised signals. However, existing GNN-based approaches implicitly follow the homophily principle (i.e., the "like attracts like" phenomenon) and fail to learn discriminative embedding for anomalies that connect vast normal nodes. Moreover, such approaches identify anomalies in a unified global perspective but overlook diversified abnormal patterns conditioned on local graph context, leading to suboptimal performance. To overcome the aforementioned limitations, in this paper, we propose a Multi-hypersphere Heterophilic Graph Learning (MHetGL) framework for unsupervised GAD. Specifically, we first devise a Heterophilic Graph Encoding (HGE) module to learn distinguishable representations for potential anomalies by purifying and augmenting their neighborhood in a fully unsupervised manner. Then, we propose a Multi-Hypersphere Learning (MHL) module to enhance the detection capability for context-dependent anomalies by jointly incorporating critical patterns from both global and local perspectives. Extensive experiments on ten real-world datasets show that MHetGL outperforms 14 baselines. Our code is publicly available at https://github.com/KennyNH/MHetGL.
Graph learning plays a vital role in mining and analyzing complex relationships involved in graph data, which is widely used in many real-world applications like transaction networks and communication networks. Foundation models in CV and NLP have shown powerful cross-domain capabilities that are also significant in graph domains. However, existing graph learning approaches struggle with cross-domain tasks. Inspired by successes in CV and NLP, cross-domain graph learning has once again become a focal point of attention to realizing true graph foundation models. In this survey, we present a comprehensive review and analysis of existing works on cross-domain graph learning. Concretely, we first propose a new taxonomy, categorizing existing approaches based on the learned cross-domain information: structure, feature, and structure-feature mixture. Next, we systematically survey representative methods in these categories. Finally, we discuss the remaining limitations of existing studies and highlight promising avenues for future research. Relevant papers are summarized and will be consistently updated at: https://github.com/cshhzhao/Awesome-Cross-Domain-Graph-Learning.
Graph similarity learning (GSL), also referred to as graph matching in many scenarios, is a fundamental problem in computer vision, pattern recognition, and graph learning. However, previous GSL methods assume that graphs are homogeneous and struggle to maintain their performance on heterogeneous graphs. To address this problem, this paper proposes a Heterogeneous Graph Matching Network (HeGMN), which is an end-to-end graph similarity learning framework composed of a two-tier matching mechanism. Firstly, a heterogeneous graph isomorphism network is proposed as the encoder, which reinvents graph isomorphism network for heterogeneous graphs by perceiving different semantic relationships during aggregation. Secondly, a graph-level and node-level matching modules are designed, both employing type-aligned matching principles. The former conducts graph-level matching by node type alignment, and the latter computes the interactions between the cross-graph nodes with the same type thus reducing noise interference and computational overhead. Finally, the graph-level and node-level matching features are combined and fed into fully connected layers for predicting graph similarity scores. In experiments, we propose a heterogeneous graph resampling method to construct heterogeneous graph pairs and define the corresponding heterogeneous graph edit distance, filling the gap in missing datasets. Extensive experiments demonstrate that HeGMN consistently achieves advanced performance on graph similarity prediction across all datasets.
Continual Graph Learning (CGL), which aims to accommodate new tasks over evolving graph data without forgetting prior knowledge, is garnering significant research interest. Mainstream solutions adopt the memory replay-based idea, ie, caching representative data from earlier tasks for retraining the graph model. However, this strategy struggles with scalability issues for constantly evolving graphs and raises concerns regarding data privacy. Inspired by recent advancements in the prompt-based learning paradigm, this paper introduces a novel prompt-driven continual graph learning (PROMPTCGL) framework, which learns a separate prompt for each incoming task and maintains the underlying graph neural network model fixed. In this way, PROMPTCGL naturally avoids catastrophic forgetting of knowledge from previous tasks. More specifically, we propose hierarchical prompting to instruct the model from both feature- and topology-level to fully address the variability of task graphs in dynamic continual learning. Additionally, we develop a personalized prompt generator to generate tailored prompts for each graph node while minimizing the number of prompts needed, leading to constant memory consumption regardless of the graph scale. Extensive experiments on four benchmarks show that PROMPTCGL achieves superior performance against existing CGL approaches while significantly reducing memory consumption. Our code is available at https://github.com/QiWang98/PromptCGL.
Urban traffic optimization is critical for improving transportation efficiency and alleviating congestion, particularly in large-scale dynamic networks. Traditional methods, such as Dijkstra's and Floyd's algorithms, provide effective solutions in static settings, but they struggle with the spatial-temporal complexity of real-world traffic flows. In this work, we propose TrafficKAN-GCN, a hybrid deep learning framework combining Kolmogorov-Arnold Networks (KAN) with Graph Convolutional Networks (GCN), designed to enhance urban traffic flow optimization. By integrating KAN's adaptive nonlinear function approximation with GCN's spatial graph learning capabilities, TrafficKAN-GCN captures both complex traffic patterns and topological dependencies. We evaluate the proposed framework using real-world traffic data from the Baltimore Metropolitan area. Compared with baseline models such as MLP-GCN, standard GCN, and Transformer-based approaches, TrafficKAN-GCN achieves competitive prediction accuracy while demonstrating improved robustness in handling noisy and irregular traffic data. Our experiments further highlight the framework's ability to redistribute traffic flow, mitigate congestion, and adapt to disruptive events, such as the Francis Scott Key Bridge collapse. This study contributes to the growing body of work on hybrid graph learning for intelligent transportation systems, highlighting the potential of combining KAN and GCN for real-time traffic optimization. Future work will focus on reducing computational overhead and integrating Transformer-based temporal modeling for enhanced long-term traffic prediction. The proposed TrafficKAN-GCN framework offers a promising direction for data-driven urban mobility management, balancing predictive accuracy, robustness, and computational efficiency.
Graph Neural Networks (GNNs) have shown remarkable success in various graph-based learning tasks. However, recent studies have raised concerns about fairness and privacy issues in GNNs, highlighting the potential for biased or discriminatory outcomes and the vulnerability of sensitive information. This paper presents a comprehensive investigation of fairness and privacy in GNNs, exploring the impact of various fairness-preserving measures on model performance. We conduct experiments across diverse datasets and evaluate the effectiveness of different fairness interventions. Our analysis considers the trade-offs between fairness, privacy, and accuracy, providing insights into the challenges and opportunities in achieving both fair and private graph learning. The results highlight the importance of carefully selecting and combining fairness-preserving measures based on the specific characteristics of the data and the desired fairness objectives. This study contributes to a deeper understanding of the complex interplay between fairness, privacy, and accuracy in GNNs, paving the way for the development of more robust and ethical graph learning models.
Graph-structured data has become increasingly prevalent across various domains, raising the demand for effective models to handle graph tasks like node classification and link prediction. Traditional graph learning models like Graph Neural Networks (GNNs) have made significant strides, but their capabilities in handling graph data remain limited in certain contexts. In recent years, large language models (LLMs) have emerged as promising candidates for graph tasks, yet most studies focus primarily on performance benchmarks and fail to address their broader potential, including their ability to handle limited data, their transferability across tasks, and their robustness. In this work, we provide a comprehensive exploration of LLMs applied to graph tasks. We evaluate the performance of pure LLMs, including those without parameter optimization and those fine-tuned with instructions, across various scenarios. Our analysis goes beyond accuracy, assessing LLM ability to perform in few-shot/zero-shot settings, transfer across domains, understand graph structures, and demonstrate robustness in challenging scenarios. We conduct extensive experiments with 16 graph learning models alongside 6 LLMs (e.g., Llama3B, GPT-4o, Qwen-plus), comparing their performance on datasets like Cora, PubMed, ArXiv, and Products. Our findings show that LLMs, particularly those with instruction tuning, outperform traditional models in few-shot settings, exhibit strong domain transferability, and demonstrate excellent generalization and robustness. This work offers valuable insights into the capabilities of LLMs for graph learning, highlighting their advantages and potential for real-world applications, and paving the way for future research in this area. Codes and datasets are released in https://github.com/myflashbarry/LLM-benchmarking.
Despite extensive research efforts focused on OOD detection on images, OOD detection on nodes in graph learning remains underexplored. The dependence among graph nodes hinders the trivial adaptation of existing approaches on images that assume inputs to be i.i.d. sampled, since many unique features and challenges specific to graphs are not considered, such as the heterophily issue. Recently, GNNSafe, which considers node dependence, adapted energy-based detection to the graph domain with state-of-the-art performance, however, it has two serious issues: 1) it derives node energy from classification logits without specifically tailored training for modeling data distribution, making it less effective at recognizing OOD data; 2) it highly relies on energy propagation, which is based on homophily assumption and will cause significant performance degradation on heterophilic graphs, where the node tends to have dissimilar distribution with its neighbors. To address the above issues, we suggest training EBMs by MLE to enhance data distribution modeling and remove energy propagation to overcome the heterophily issues. However, training EBMs via MLE requires performing MCMC sampling on both node feature and node neighbors, which is challenging due to the node interdependence and discrete graph topology. To tackle the sampling challenge, we introduce DeGEM, which decomposes the learning process into two parts: a graph encoder that leverages topology information for node representations and an energy head that operates in latent space. Extensive experiments validate that DeGEM, without OOD exposure during training, surpasses previous state-of-the-art methods, achieving an average AUROC improvement of 6.71% on homophilic graphs and 20.29% on heterophilic graphs, and even outperform methods trained with OOD exposure. Our code is available at: https://github.com/draym28/DeGEM.