In recent years, traffic flow prediction has played a crucial role in the management of intelligent transportation systems. However, traditional forecasting methods often model non-Euclidean low-dimensional traffic data as a simple graph with single-type nodes and edges, failing to capture similar trends among nodes of the same type. To address this limitation, this paper proposes MHGNet, a novel framework for modeling spatiotemporal multi-heterogeneous graphs. Within this framework, the STD Module decouples single-pattern traffic data into multi-pattern traffic data through feature mappings of timestamp embedding matrices and node embedding matrices. Subsequently, the Node Clusterer leverages the Euclidean distance between nodes and different types of limit points to perform clustering with O(N) time complexity. The nodes within each cluster undergo residual subgraph convolution within the spatiotemporal fusion subgraphs generated by the DSTGG Module, followed by processing in the SIE Module for node repositioning and redistribution of weights. To validate the effectiveness of MHGNet, this paper conducts extensive ablation studies and quantitative evaluations on four widely used benchmarks, demonstrating its superior performance.
Transformers have set new benchmarks in audio processing tasks, leveraging self-attention mechanisms to capture complex patterns and dependencies within audio data. However, their focus on pairwise interactions limits their ability to process the higher-order relations essential for identifying distinct audio objects. To address this limitation, this work introduces the Local- Higher Order Graph Neural Network (LHGNN), a graph based model that enhances feature understanding by integrating local neighbourhood information with higher-order data from Fuzzy C-Means clusters, thereby capturing a broader spectrum of audio relationships. Evaluation of the model on three publicly available audio datasets shows that it outperforms Transformer-based models across all benchmarks while operating with substantially fewer parameters. Moreover, LHGNN demonstrates a distinct advantage in scenarios lacking ImageNet pretraining, establishing its effectiveness and efficiency in environments where extensive pretraining data is unavailable.
Efficient prediction of default risk for bond-issuing enterprises is pivotal for maintaining stability and fostering growth in the bond market. Conventional methods usually rely solely on an enterprise's internal data for risk assessment. In contrast, graph-based techniques leverage interconnected corporate information to enhance default risk identification for targeted bond issuers. Traditional graph techniques such as label propagation algorithm or deepwalk fail to effectively integrate a enterprise's inherent attribute information with its topological network data. Additionally, due to data scarcity and security privacy concerns between enterprises, end-to-end graph neural network (GNN) algorithms may struggle in delivering satisfactory performance for target tasks. To address these challenges, we present a novel two-stage model. In the first stage, we employ an innovative Masked Autoencoders for Heterogeneous Graph (HGMAE) to pre-train on a vast enterprise knowledge graph. Subsequently, in the second stage, a specialized classifier model is trained to predict default risk propagation probabilities. The classifier leverages concatenated feature vectors derived from the pre-trained encoder with the enterprise's task-specific feature vectors. Through the two-stage training approach, our model not only boosts the importance of unique bond characteristics for specific default prediction tasks, but also securely and efficiently leverage the global information pre-trained from other enterprises. Experimental results demonstrate that our proposed model outperforms existing approaches in predicting default risk for bond issuers.
Micro-video recommendation is attracting global attention and becoming a popular daily service for people of all ages. Recently, Graph Neural Networks-based micro-video recommendation has displayed performance improvement for many kinds of recommendation tasks. However, the existing works fail to fully consider the characteristics of micro-videos, such as the high timeliness of news nature micro-video recommendation and sequential interactions of frequently changed interests. In this paper, a novel Multi-aggregator Time-warping Heterogeneous Graph Neural Network (MTHGNN) is proposed for personalized news nature micro-video recommendation based on sequential sessions, where characteristics of micro-videos are comprehensively studied, users' preference is mined via multi-aggregator, the temporal and dynamic changes of users' preference are captured, and timeliness is considered. Through the comparison with the state-of-the-arts, the experimental results validate the superiority of our MTHGNN model.
Graph neural networks (GNNs) have demonstrated superior performance in collaborative recommendation through their ability to conduct high-order representation smoothing, effectively capturing structural information within users' interaction patterns. However, existing GNN paradigms face significant challenges in scalability and robustness when handling large-scale, noisy, and real-world datasets. To address these challenges, we present LightGNN, a lightweight and distillation-based GNN pruning framework designed to substantially reduce model complexity while preserving essential collaboration modeling capabilities. Our LightGNN framework introduces a computationally efficient pruning module that adaptively identifies and removes redundant edges and embedding entries for model compression. The framework is guided by a resource-friendly hierarchical knowledge distillation objective, whose intermediate layer augments the observed graph to maintain performance, particularly in high-rate compression scenarios. Extensive experiments on public datasets demonstrate LightGNN's effectiveness, significantly improving both computational efficiency and recommendation accuracy. Notably, LightGNN achieves an 80% reduction in edge count and 90% reduction in embedding entries while maintaining performance comparable to more complex state-of-the-art baselines. The implementation of our LightGNN framework is available at the github repository: https://github.com/HKUDS/LightGNN.
Advanced Persistent Threats (APTs) represent a significant challenge in cybersecurity due to their sophisticated and stealthy nature. Traditional Intrusion Detection Systems (IDS) often fall short in detecting these multi-stage attacks. Recently, Graph Neural Networks (GNNs) have been employed to enhance IDS capabilities by analyzing the complex relationships within networked data. However, existing GNN-based solutions are hampered by high false positive rates and substantial resource consumption. In this paper, we present a novel IDS designed to detect APTs using a Spatio-Temporal Graph Neural Network Autoencoder. Our approach leverages spatial information to understand the interactions between entities within a graph and temporal information to capture the evolution of the graph over time. This dual perspective is crucial for identifying the sequential stages of APTs. Furthermore, to address privacy and scalability concerns, we deploy our architecture in a federated learning environment. This setup ensures that local data remains on-premise while encrypted model-weights are shared and aggregated using homomorphic encryption, maintaining data privacy and security. Our evaluation shows that this system effectively detects APTs with lower false positive rates and optimized resource usage compared to existing methods, highlighting the potential of spatio-temporal analysis and federated learning in enhancing cybersecurity defenses.
Major depressive disorder (MDD) is one of the most common mental disorders, with significant impacts on many daily activities and quality of life. It stands as one of the most common mental disorders globally and ranks as the second leading cause of disability. The current diagnostic approach for MDD primarily relies on clinical observations and patient-reported symptoms, overlooking the diverse underlying causes and pathophysiological factors contributing to depression. Therefore, scientific researchers and clinicians must gain a deeper understanding of the pathophysiological mechanisms involved in MDD. There is growing evidence in neuroscience that depression is a brain network disorder, and the use of neuroimaging, such as magnetic resonance imaging (MRI), plays a significant role in identifying and treating MDD. Rest-state functional MRI (rs-fMRI) is among the most popular neuroimaging techniques used to study MDD. Deep learning techniques have been widely applied to neuroimaging data to help with early mental health disorder detection. Recent years have seen a rise in interest in graph neural networks (GNNs), which are deep neural architectures specifically designed to handle graph-structured data like rs-fMRI. This research aimed to develop an ensemble-based GNN model capable of detecting discriminative features from rs-fMRI images for the purpose of diagnosing MDD. Specifically, we constructed an ensemble model by combining features from multiple brain region segmentation atlases to capture brain complexity and detect distinct features more accurately than single atlas-based models. Further, the effectiveness of our model is demonstrated by assessing its performance on a large multi-site MDD dataset. The best performing model among all folds achieved an accuracy of 75.80%, a sensitivity of 88.89%, a specificity of 61.84%, a precision of 71.29%, and an F1-score of 79.12%.
Graph neural network universal interatomic potentials (GNN-UIPs) have demonstrated remarkable generalization and transfer capabilities in material discovery and property prediction. These models can accelerate molecular dynamics (MD) simulation by several orders of magnitude while maintaining \textit{ab initio} accuracy, making them a promising new paradigm in material simulations. One notable example is Crystal Hamiltonian Graph Neural Network (CHGNet), pretrained on the energies, forces, stresses, and magnetic moments from the MPtrj dataset, representing a state-of-the-art GNN-UIP model for charge-informed MD simulations. However, training the CHGNet model is time-consuming(8.3 days on one A100 GPU) for three reasons: (i) requiring multi-layer propagation to reach more distant atom information, (ii) requiring second-order derivatives calculation to finish weights updating and (iii) the implementation of reference CHGNet does not fully leverage the computational capabilities. This paper introduces FastCHGNet, an optimized CHGNet, with three contributions: Firstly, we design innovative Force/Stress Readout modules to decompose Force/Stress prediction. Secondly, we adopt massive optimizations such as kernel fusion, redundancy bypass, etc, to exploit GPU computation power sufficiently. Finally, we extend CHGNet to support multiple GPUs and propose a load-balancing technique to enhance GPU utilization. Numerical results show that FastCHGNet reduces memory footprint by a factor of 3.59. The final training time of FastCHGNet can be decreased to \textbf{1.53 hours} on 32 GPUs without sacrificing model accuracy.
One of the important factors affecting micro-video recommender systems is to model the multi-modal user preference on the micro-video. Despite the remarkable performance of prior arts, they are still limited by fusing the user preference derived from different modalities in a unified manner, ignoring the users tend to place different emphasis on different modalities. Furthermore, modality-missing is ubiquity and unavoidable in the micro-video recommendation, some modalities information of micro-videos are lacked in many cases, which negatively affects the multi-modal fusion operations. To overcome these disadvantages, we propose a novel framework for the micro-video recommendation, dubbed Dual Graph Neural Network (DualGNN), upon the user-microvideo bipartite and user co-occurrence graphs, which leverages the correlation between users to collaboratively mine the particular fusion pattern for each user. Specifically, we first introduce a single-modal representation learning module, which performs graph operations on the user-microvideo graph in each modality to capture single-modal user preferences on different modalities. And then, we devise a multi-modal representation learning module to explicitly model the user’s attentions over different modalities and inductively learn the multi-modal user preference. Finally, we propose a prediction module to rank the potential micro-videos for users. Extensive experiments on two public datasets demonstrate the significant superiority of our DualGNN over state-of-the-arts methods.
Class imbalance is pervasive in real-world graph datasets, where the majority of annotated nodes belong to a small set of classes (majority classes), leaving many other classes (minority classes) with only a handful of labeled nodes. Graph Neural Networks (GNNs) suffer from significant performance degradation in the presence of class imbalance, exhibiting bias towards majority classes and struggling to generalize effectively on minority classes. This limitation stems, in part, from the message passing process, leading GNNs to overfit to the limited neighborhood of annotated nodes from minority classes and impeding the propagation of discriminative information throughout the entire graph. In this paper, we introduce a novel Unified Graph Neural Network Learning (Uni-GNN) framework to tackle class-imbalanced node classification. The proposed framework seamlessly integrates both structural and semantic connectivity representations through semantic and structural node encoders. By combining these connectivity types, Uni-GNN extends the propagation of node embeddings beyond immediate neighbors, encompassing non-adjacent structural nodes and semantically similar nodes, enabling efficient diffusion of discriminative information throughout the graph. Moreover, to harness the potential of unlabeled nodes within the graph, we employ a balanced pseudo-label generation mechanism that augments the pool of available labeled nodes from minority classes in the training set. Experimental results underscore the superior performance of our proposed Uni-GNN framework compared to state-of-the-art class-imbalanced graph learning baselines across multiple benchmark datasets.
Federated Graph Learning (FGL) has demonstrated the advantage of training a global Graph Neural Network (GNN) model across distributed clients using their local graph data. Unlike Euclidean data (\eg, images), graph data is composed of nodes and edges, where the overall node-edge connections determine the topological structure, and individual nodes along with their neighbors capture local node features. However, existing studies tend to prioritize one aspect over the other, leading to an incomplete understanding of the data and the potential misidentification of key characteristics across varying graph scenarios. Additionally, the non-independent and identically distributed (non-IID) nature of graph data makes the extraction of these two data characteristics even more challenging. To address the above issues, we propose a novel FGL framework, named FedGCF, which aims to simultaneously extract and fuse structural properties and node features to effectively handle diverse graph scenarios. FedGCF first clusters clients by structural similarity, performing model aggregation within each cluster to form the shared structural model. Next, FedGCF selects the clients with common node features and aggregates their models to generate a common node model. This model is then propagated to all clients, allowing common node features to be shared. By combining these two models with a proper ratio, FedGCF can achieve a comprehensive understanding of the graph data and deliver better performance, even under non-IID distributions. Experimental results show that FedGCF improves accuracy by 4.94%-7.24% under different data distributions and reduces communication cost by 64.18%-81.25% to reach the same accuracy compared to baselines.
Approximation-based spectral graph neural networks, which construct graph filters with function approximation, have shown substantial performance in graph learning tasks. Despite their great success, existing works primarily employ polynomial approximation to construct the filters, whereas another superior option, namely ration approximation, remains underexplored. Although a handful of prior works have attempted to deploy the rational approximation, their implementations often involve intensive computational demands or still resort to polynomial approximations, hindering full potential of the rational graph filters. To address the issues, this paper introduces ERGNN, a novel spectral GNN with explicitly-optimized rational filter. ERGNN adopts a unique two-step framework that sequentially applies the numerator filter and the denominator filter to the input signals, thus streamlining the model paradigm while enabling explicit optimization of both numerator and denominator of the rational filter. Extensive experiments validate the superiority of ERGNN over state-of-the-art methods, establishing it as a practical solution for deploying rational-based GNNs.
Drug-target interaction is fundamental in understanding how drugs affect biological systems, and accurately predicting drug-target affinity (DTA) is vital for drug discovery. Recently, deep learning methods have emerged as a significant approach for estimating the binding strength between drugs and target proteins. However, existing methods simply utilize the drug's local information from molecular topology rather than global information. Additionally, the features of drugs and proteins are usually fused with a simple concatenation operation, limiting their effectiveness. To address these challenges, we proposed ViDTA, an enhanced DTA prediction framework. We introduce virtual nodes into the Graph Neural Network (GNN)-based drug feature extraction network, which acts as a global memory to exchange messages more efficiently. By incorporating virtual graph nodes, we seamlessly integrate local and global features of drug molecular structures, expanding the GNN's receptive field. Additionally, we propose an attention-based linear feature fusion network for better capturing the interaction information between drugs and proteins. Experimental results evaluated on various benchmarks including Davis, Metz, and KIBA demonstrate that our proposed ViDTA outperforms the state-of-the-art baselines.
Real-world graph data environments intrinsically exist noise (e.g., link and structure errors) that inevitably disturb the effectiveness of graph representation and downstream learning tasks. For homogeneous graphs, the latest works use original node features to synthesize a similarity graph that can correct the structure of the noised graph. This idea is based on the homogeneity assumption, which states that similar nodes in the homogeneous graph tend to have direct links in the original graph. However, similar nodes in heterogeneous graphs usually do not have direct links, which can not be used to correct the original noise graph. This causes a significant challenge in noised heterogeneous graph learning. To this end, this paper proposes a novel synthesized similarity-based graph neural network compatible with noised heterogeneous graph learning. First, we calculate the original feature similarities of all nodes to synthesize a similarity-based high-order graph. Second, we propose a similarity-aware encoder to embed original and synthesized graphs with shared parameters. Then, instead of graph-to-graph supervising, we synchronously supervise the original and synthesized graph embeddings to predict the same labels. Meanwhile, a target-based graph extracted from the synthesized graph contrasts the structure of the metapath-based graph extracted from the original graph to learn the mutual information. Extensive experiments in numerous real-world datasets show the proposed method achieves state-of-the-art records in the noised heterogeneous graph learning tasks. In highlights, +5$\sim$6\% improvements are observed in several noised datasets compared with previous SOTA methods. The code and datasets are available at https://github.com/kg-cc/NoiseHGNN.
Feature-based image matching has extensive applications in computer vision. Keypoints detected in images can be naturally represented as graph structures, and Graph Neural Networks (GNNs) have been shown to outperform traditional deep learning techniques. Consequently, the paradigm of image matching via GNNs has gained significant prominence in recent academic research. In this paper, we first introduce an innovative adaptive graph construction method that utilizes a filtering mechanism based on distance and dynamic threshold similarity. This method dynamically adjusts the criteria for incorporating new vertices based on the characteristics of existing vertices, allowing for the construction of more precise and robust graph structures while avoiding redundancy. We further combine the vertex processing capabilities of GNNs with the global awareness capabilities of Transformers to enhance the model's representation of spatial and feature information within graph structures. This hybrid model provides a deeper understanding of the interrelationships between vertices and their contributions to the matching process. Additionally, we employ the Sinkhorn algorithm to iteratively solve for optimal matching results. Finally, we validate our system using extensive image datasets and conduct comprehensive comparative experiments. Experimental results demonstrate that our system achieves an average improvement of 3.8x-40.3x in overall matching performance. Additionally, the number of vertices and edges significantly impacts training efficiency and memory usage; therefore, we employ multi-GPU technology to accelerate the training process. Our code is available at https://github.com/songxf1024/GIMS.
Credit card fraud incurs a considerable cost for both cardholders and issuing banks. Contemporary methods apply machine learning-based classifiers to detect fraudulent behavior from labeled transaction records. But labeled data are usually a small proportion of billions of real transactions due to expensive labeling costs, which implies that they do not well exploit many natural features from unlabeled data. Therefore, we propose a semi-supervised graph neural network for fraud detection. Specifically, we leverage transaction records to construct a temporal transaction graph, which is composed of temporal transactions (nodes) and interactions (edges) among them. Then we pass messages among the nodes through a Gated Temporal Attention Network (GTAN) to learn the transaction representation. We further model the fraud patterns through risk propagation among transactions. The extensive experiments are conducted on a real-world transaction dataset and two publicly available fraud detection datasets. The result shows that our proposed method, namely GTAN, outperforms other state-of-the-art baselines on three fraud detection datasets. Semi-supervised experiments demonstrate the excellent fraud detection performance of our model with only a tiny proportion of labeled data.
Parametric message passing (MP) is a promising technique that provides reliable marginal probability distributions for distributed cooperative positioning (DCP) based on factor graphs (FG), while maintaining minimal computational complexity. However, conventional parametric MP-based DCP methods may fail to converge in dense wireless networks due to numerous short loops on FG. Additionally, the use of inappropriate message approximation techniques can lead to increased sensitivity to initial values and significantly slower convergence rates. To address the challenging DCP problem modeled by a loopy FG, we propose an effective graph neural network enhanced fast convergent parametric MP (GNN--FCPMP) method. We first employ Chebyshev polynomials to approximate the nonlinear terms present in the FG-based spatio-temporal messages. This technique facilitates the derivation of globally precise, closed-form representations for each message transmitted across the FG. Then, the parametric representations of spatial messages are meticulously refined through data-driven graph neural networks (GNNs). Conclusively, by performing inference on the FG, we derive more accurate closed-form expressions for the a posteriori distributions of node positions. Numerical results substantiate the capability of GNN--FCPMP to significantly enhance positioning accuracy within wireless networks characterized by high-density loops and ensure rapid convergence.
Classifying antimicrobial peptides(AMPs) from the vast array of peptides mined from metagenomic sequencing data is a significant approach to addressing the issue of antibiotic resistance. However, current AMP classification methods, primarily relying on sequence-based data, neglect the spatial structure of peptides, thereby limiting the accurate classification of AMPs. Additionally, the number of known AMPs is significantly lower than that of non-AMPs, leading to imbalanced datasets that reduce predictive accuracy for AMPs. To alleviate these two limitations, we first employ Omegafold to predict the three-dimensional spatial structures of AMPs and non-AMPs, constructing peptide graphs based on the amino acids' C$_\alpha$ positions. Building upon this, we propose a novel classification model named Spatial GNN-based AMP Classifier (SGAC). Our SGAC model employs a graph encoder based on Graph Neural Networks (GNNs) to process peptide graphs, generating high-dimensional representations that capture essential features from the three-dimensional spatial structure of amino acids. Then, to address the inherent imbalanced datasets, SGAC first incorporates Weight-enhanced Contrastive Learning, which clusters similar peptides while ensuring separation between dissimilar ones, using weighted contributions to emphasize AMP-specific features. Furthermore, SGAC employs Weight-enhanced Pseudo-label Distillation to dynamically generate high-confidence pseudo labels for ambiguous peptides, further refining predictions and promoting balanced learning between AMPs and non-AMPs. Experiments on publicly available AMP and non-AMP datasets demonstrate that SGAC significantly outperforms traditional sequence-based methods and achieves state-of-the-art performance among graph-based models, validating its effectiveness in AMP classification.
We put forth a principled design of a neural architecture to learn nodal Adjacency Spectral Embeddings (ASE) from graph inputs. By bringing to bear the gradient descent (GD) method and leveraging the principle of algorithm unrolling, we truncate and re-interpret each GD iteration as a layer in a graph neural network (GNN) that is trained to approximate the ASE. Accordingly, we call the resulting embeddings and our parametric model Learned ASE (LASE), which is interpretable, parameter efficient, robust to inputs with unobserved edges, and offers controllable complexity during inference. LASE layers combine Graph Convolutional Network (GCN) and fully-connected Graph Attention Network (GAT) modules, which is intuitively pleasing since GCN-based local aggregations alone are insufficient to express the sought graph eigenvectors. We propose several refinements to the unrolled LASE architecture (such as sparse attention in the GAT module and decoupled layerwise parameters) that offer favorable approximation error versus computation tradeoffs; even outperforming heavily-optimized eigendecomposition routines from scientific computing libraries. Because LASE is a differentiable function with respect to its parameters as well as its graph input, we can seamlessly integrate it as a trainable module within a larger (semi-)supervised graph representation learning pipeline. The resulting end-to-end system effectively learns ``discriminative ASEs'' that exhibit competitive performance in supervised link prediction and node classification tasks, outperforming a GNN even when the latter is endowed with open loop, meaning task-agnostic, precomputed spectral positional encodings.
Anomaly detection using a network-based approach is one of the most efficient ways to identify abnormal events such as fraud, security breaches, and system faults in a variety of applied domains. While most of the earlier works address the complex nature of graph-structured data and predefined anomalies, the impact of data attributes and emerging anomalies are often neglected. This paper introduces DCOR, a novel approach on attributed networks that integrates reconstruction-based anomaly detection with Contrastive Learning. Utilizing a Graph Neural Network (GNN) framework, DCOR contrasts the reconstructed adjacency and feature matrices from both the original and augmented graphs to detect subtle anomalies. We employed comprehensive experimental studies on benchmark datasets through standard evaluation measures. The results show that DCOR significantly outperforms state-of-the-art methods. Obtained results demonstrate the efficacy of proposed approach in attributed networks with the potential of uncovering new patterns of anomalies.