Cycles are fundamental elements in graph-structured data and have demonstrated their effectiveness in enhancing graph learning models. To encode such information into a graph learning framework, prior works often extract a summary quantity, ranging from the number of cycles to the more sophisticated persistence diagram summaries. However, more detailed information, such as which edges are encoded in a cycle, has not yet been used in graph neural networks. In this paper, we make one step towards addressing this gap, and propose a structure encoding module, called CycleNet, that encodes cycle information via edge structure encoding in a permutation invariant manner. To efficiently encode the space of all cycles, we start with a cycle basis (i.e., a minimal set of cycles generating the cycle space) which we compute via the kernel of the 1-dimensional Hodge Laplacian of the input graph. To guarantee the encoding is invariant w.r.t. the choice of cycle basis, we encode the cycle information via the orthogonal projector of the cycle basis, which is inspired by BasisNet proposed by Lim et al. We also develop a more efficient variant which however requires that the input graph has a unique shortest cycle basis. To demonstrate the effectiveness of the proposed module, we provide some theoretical understandings of its expressive power. Moreover, we show via a range of experiments that networks enhanced by our CycleNet module perform better in various benchmarks compared to several existing SOTA models.
Resting-state fMRI (rs-fMRI) functional connectivity (FC) analysis provides valuable insights into the relationships between different brain regions and their potential implications for neurological or psychiatric disorders. However, specific design efforts to predict treatment response from rs-fMRI remain limited due to difficulties in understanding the current brain state and the underlying mechanisms driving the observed patterns, which limited the clinical application of rs-fMRI. To overcome that, we propose a graph learning framework that captures comprehensive features by integrating both correlation and distance-based similarity measures under a contrastive loss. This approach results in a more expressive framework that captures brain dynamic features at different scales and enables more accurate prediction of treatment response. Our experiments on the chronic pain and depersonalization disorder datasets demonstrate that our proposed method outperforms current methods in different scenarios. To the best of our knowledge, we are the first to explore the integration of distance-based and correlation-based neural similarity into graph learning for treatment response prediction.
In-vehicle network (IVN) is facing complex external cyber-attacks, especially the emerging masquerade attacks with extremely high difficulty of detection while serious damaging effects. In this paper, we propose the STATGRAPH, which is an effective and fine-grained intrusion detection methodology for IVN security services via multi-view statistical graph learning on in-vehicle controller area network (CAN) messages with insight into their variations in periodicity, payload and signal combinations. Specifically, STATGRAPH generates two statistical graphs, timing correlation graph (TCG) and coupling relationship graph (CRG), in every CAN message detection window, where edge attributes in TCGs represent temporal correlation between different message IDs while edge attributes in CRGs denote the neighbour relationship and contextual similarity. Besides, a lightweight shallow layered graph convolution network is trained based on graph property of TCGs and CRGs, which learns the universal laws of various patterns more effectively and further enhance the performance of detection. To address the problem of insufficient attack types in previous intrusion detection, we select two real in-vehicle CAN datasets covering five new instances of sophisticated and stealthy masquerade attacks that are never investigated before. Experimental result shows STATGRAPH improves both detection granularity and detection performance over state-of-the-art intrusion detection methods. Code is available at https://github.com/wangkai-tech23/StatGraph.
The complexity of modern hardware designs necessitates advanced methodologies for optimizing and analyzing modern digital systems. In recent times, machine learning (ML) methodologies have emerged as potent instruments for assessing design quality-of-results at the Register-Transfer Level (RTL) or Boolean level, aiming to expedite design exploration of advanced RTL configurations. In this presentation, we introduce an innovative open-source framework that translates RTL designs into graph representation foundations, which can be seamlessly integrated with the PyTorch Geometric graph learning platform. Furthermore, the Verilog-to-PyG (V2PYG) framework is compatible with the open-source Electronic Design Automation (EDA) toolchain OpenROAD, facilitating the collection of labeled datasets in an utterly open-source manner. Additionally, we will present novel RTL data augmentation methods (incorporated in our framework) that enable functional equivalent design augmentation for the construction of an extensive graph-based RTL design database. Lastly, we will showcase several using cases of V2PYG with detailed scripting examples. V2PYG can be found at \url{https://yu-maryland.github.io/Verilog-to-PyG/}.
The principal benefit of unsupervised representation learning is that a pre-trained model can be fine-tuned where data or labels are scarce. Existing approaches for graph representation learning are domain specific, maintaining consistent node and edge features across the pre-training and target datasets. This has precluded transfer to multiple domains. We present Topology Only Pre-Training (ToP), a graph pre-training method based on node and edge feature exclusion. We show positive transfer on evaluation datasets from multiple domains, including domains not present in pre-training data, running directly contrary to assumptions made in contemporary works. On 75% of experiments, ToP models perform significantly $p \leq 0.01$ better than a supervised baseline. Performance is significantly positive on 85.7% of tasks when node and edge features are used in fine-tuning. We further show that out-of-domain topologies can produce more useful pre-training than in-domain. Under ToP we show better transfer from non-molecule pre-training, compared to molecule pre-training, on 79% of molecular benchmarks. Against the limited set of other generalist graph models ToP performs strongly, including against models with many orders of magnitude larger. These findings show that ToP opens broad areas of research in both transfer learning on scarcely populated graph domains and in graph foundation models.
The sequential recommendation system has been widely studied for its promising effectiveness in capturing dynamic preferences buried in users' sequential behaviors. Despite the considerable achievements, existing methods usually focus on intra-sequence modeling while overlooking exploiting global collaborative information by inter-sequence modeling, resulting in inferior recommendation performance. Therefore, previous works attempt to tackle this problem with a global collaborative item graph constructed by pre-defined rules. However, these methods neglect two crucial properties when capturing global collaborative information, i.e., adaptiveness and personalization, yielding sub-optimal user representations. To this end, we propose a graph-driven framework, named Adaptive and Personalized Graph Learning for Sequential Recommendation (APGL4SR), that incorporates adaptive and personalized global collaborative information into sequential recommendation systems. Specifically, we first learn an adaptive global graph among all items and capture global collaborative information with it in a self-supervised fashion, whose computational burden can be further alleviated by the proposed SVD-based accelerator. Furthermore, based on the graph, we propose to extract and utilize personalized item correlations in the form of relative positional encoding, which is a highly compatible manner of personalizing the utilization of global collaborative information. Finally, the entire framework is optimized in a multi-task learning paradigm, thus each part of APGL4SR can be mutually reinforced. As a generic framework, APGL4SR can outperform other baselines with significant margins. The code is available at https://github.com/Graph-Team/APGL4SR.
Graph Neural Networks (GNNs) have emerged as a prominent graph learning model in various graph-based tasks over the years. Nevertheless, due to the vulnerabilities of GNNs, it has been empirically proved that malicious attackers could easily corrupt the fairness level of their predictions by adding perturbations to the input graph data. In this paper, we take crucial steps to study a novel problem of certifiable defense on the fairness level of GNNs. Specifically, we propose a principled framework named ELEGANT and present a detailed theoretical certification analysis for the fairness of GNNs. ELEGANT takes any GNNs as its backbone, and the fairness level of such a backbone is theoretically impossible to be corrupted under certain perturbation budgets for attackers. Notably, ELEGANT does not have any assumption over the GNN structure or parameters, and does not require re-training the GNNs to realize certification. Hence it can serve as a plug-and-play framework for any optimized GNNs ready to be deployed. We verify the satisfactory effectiveness of ELEGANT in practice through extensive experiments on real-world datasets across different backbones of GNNs, where ELEGANT is also demonstrated to be beneficial for GNN debiasing. Open-source code can be found at https://github.com/yushundong/ELEGANT.
Graph research, the systematic study of interconnected data points represented as graphs, plays a vital role in capturing intricate relationships within networked systems. However, in the real world, as graphs scale up, concerns about data security among different data-owning agencies arise, hindering information sharing and, ultimately, the utilization of graph data. Therefore, establishing a mutual trust mechanism among graph agencies is crucial for unlocking the full potential of graphs. Here, we introduce a Cooperative Network Learning (CNL) framework to ensure secure graph computing for various graph tasks. Essentially, this CNL framework unifies the local and global perspectives of GNN computing with distributed data for an agency by virtually connecting all participating agencies as a global graph without a fixed central coordinator. Inter-agency computing is protected by various technologies inherent in our framework, including homomorphic encryption and secure transmission. Moreover, each agency has a fair right to design or employ various graph learning models from its local or global perspective. Thus, CNL can collaboratively train GNN models based on decentralized graphs inferred from local and global graphs. Experiments on contagion dynamics prediction and traditional graph tasks (i.e., node classification and link prediction) demonstrate that our CNL architecture outperforms state-of-the-art GNNs developed at individual sites, revealing that CNL can provide a reliable, fair, secure, privacy-preserving, and global perspective to build effective and personalized models for network applications. We hope this framework will address privacy concerns in graph-related research and integrate decentralized graph data structures to benefit the network research community in cooperation and innovation.
Few-shot class-incremental learning (FSCIL) aims to build machine learning model that can continually learn new concepts from a few data samples, without forgetting knowledge of old classes. The challenges of FSCIL lies in the limited data of new classes, which not only lead to significant overfitting issues but also exacerbates the notorious catastrophic forgetting problems. As proved in early studies, building sample relationships is beneficial for learning from few-shot samples. In this paper, we promote the idea to the incremental scenario, and propose a Sample-to-Class (S2C) graph learning method for FSCIL. Specifically, we propose a Sample-level Graph Network (SGN) that focuses on analyzing sample relationships within a single session. This network helps aggregate similar samples, ultimately leading to the extraction of more refined class-level features. Then, we present a Class-level Graph Network (CGN) that establishes connections across class-level features of both new and old classes. This network plays a crucial role in linking the knowledge between different sessions and helps improve overall learning in the FSCIL scenario. Moreover, we design a multi-stage strategy for training S2C model, which mitigates the training challenges posed by limited data in the incremental process. The multi-stage training strategy is designed to build S2C graph from base to few-shot stages, and improve the capacity via an extra pseudo-incremental stage. Experiments on three popular benchmark datasets show that our method clearly outperforms the baselines and sets new state-of-the-art results in FSCIL.
The widespread deployment of Graph Neural Networks (GNNs) sparks significant interest in their explainability, which plays a vital role in model auditing and ensuring trustworthy graph learning. The objective of GNN explainability is to discern the underlying graph structures that have the most significant impact on model predictions. Ensuring that explanations generated are reliable necessitates consideration of the in-distribution property, particularly due to the vulnerability of GNNs to out-of-distribution data. Unfortunately, prevailing explainability methods tend to constrain the generated explanations to the structure of the original graph, thereby downplaying the significance of the in-distribution property and resulting in explanations that lack reliability. To address these challenges, we propose D4Explainer, a novel approach that provides in-distribution GNN explanations for both counterfactual and model-level explanation scenarios. The proposed D4Explainer incorporates generative graph distribution learning into the optimization objective, which accomplishes two goals: 1) generate a collection of diverse counterfactual graphs that conform to the in-distribution property for a given instance, and 2) identify the most discriminative graph patterns that contribute to a specific class prediction, thus serving as model-level explanations. It is worth mentioning that D4Explainer is the first unified framework that combines both counterfactual and model-level explanations. Empirical evaluations conducted on synthetic and real-world datasets provide compelling evidence of the state-of-the-art performance achieved by D4Explainer in terms of explanation accuracy, faithfulness, diversity, and robustness.
Node centralities play a pivotal role in network science, social network analysis, and recommender systems. In temporal data, static path-based centralities like closeness or betweenness can give misleading results about the true importance of nodes in a temporal graph. To address this issue, temporal generalizations of betweenness and closeness have been defined that are based on the shortest time-respecting paths between pairs of nodes. However, a major issue of those generalizations is that the calculation of such paths is computationally expensive. Addressing this issue, we study the application of De Bruijn Graph Neural Networks (DBGNN), a time-aware graph neural network architecture, to predict temporal path-based centralities in time series data. We experimentally evaluate our approach in 13 temporal graphs from biological and social systems and show that it considerably improves the prediction of betweenness and closeness centrality compared to (i) a static Graph Convolutional Neural Network, (ii) an efficient sampling-based approximation technique for temporal betweenness, and (iii) two state-of-the-art time-aware graph learning techniques for dynamic graphs.
We study deceptive fairness attacks on graphs to answer the following question: How can we achieve poisoning attacks on a graph learning model to exacerbate the bias deceptively? We answer this question via a bi-level optimization problem and propose a meta learning-based framework named FATE. FATE is broadly applicable with respect to various fairness definitions and graph learning models, as well as arbitrary choices of manipulation operations. We further instantiate FATE to attack statistical parity and individual fairness on graph neural networks. We conduct extensive experimental evaluations on real-world datasets in the task of semi-supervised node classification. The experimental results demonstrate that FATE could amplify the bias of graph neural networks with or without fairness consideration while maintaining the utility on the downstream task. We hope this paper provides insights into the adversarial robustness of fair graph learning and can shed light on designing robust and fair graph learning in future studies.
In recommendation, graph-based Collaborative Filtering (CF) methods mitigate the data sparsity by introducing Graph Contrastive Learning (GCL). However, the random negative sampling strategy in these GCL-based CF models neglects the semantic structure of users (items), which not only introduces false negatives (negatives that are similar to anchor user (item)) but also ignores the potential positive samples. To tackle the above issues, we propose Topology-aware Debiased Self-supervised Graph Learning (TDSGL) for recommendation, which constructs contrastive pairs according to the semantic similarity between users (items). Specifically, since the original user-item interaction data commendably reflects the purchasing intent of users and certain characteristics of items, we calculate the semantic similarity between users (items) on interaction data. Then, given a user (item), we construct its negative pairs by selecting users (items) which embed different semantic structures to ensure the semantic difference between the given user (item) and its negatives. Moreover, for a user (item), we design a feature extraction module that converts other semantically similar users (items) into an auxiliary positive sample to acquire a more informative representation. Experimental results show that the proposed model outperforms the state-of-the-art models significantly on three public datasets. Our model implementation codes are available at https://github.com/malajikuai/TDSGL.
Accurate forecasting and analysis of emerging pandemics play a crucial role in effective public health management and decision-making. Traditional approaches primarily rely on epidemiological data, overlooking other valuable sources of information that could act as sensors or indicators of pandemic patterns. In this paper, we propose a novel framework called MGL4MEP that integrates temporal graph neural networks and multi-modal data for learning and forecasting. We incorporate big data sources, including social media content, by utilizing specific pre-trained language models and discovering the underlying graph structure among users. This integration provides rich indicators of pandemic dynamics through learning with temporal graph neural networks. Extensive experiments demonstrate the effectiveness of our framework in pandemic forecasting and analysis, outperforming baseline methods across different areas, pandemic situations, and prediction horizons. The fusion of temporal graph learning and multi-modal data enables a comprehensive understanding of the pandemic landscape with less time lag, cheap cost, and more potential information indicators.
Heterogeneous Graph Neural Networks (HGNNs) are powerful tools for deep learning on heterogeneous graphs. Typical HGNNs require repetitive message passing during training, limiting efficiency for large-scale real-world graphs. Recent pre-computation-based HGNNs use one-time message passing to transform a heterogeneous graph into regular-shaped tensors, enabling efficient mini-batch training. Existing pre-computation-based HGNNs can be mainly categorized into two styles, which differ in how much information loss is allowed and efficiency. We propose a hybrid pre-computation-based HGNN, named Random Projection Heterogeneous Graph Neural Network (RpHGNN), which combines the benefits of one style's efficiency with the low information loss of the other style. To achieve efficiency, the main framework of RpHGNN consists of propagate-then-update iterations, where we introduce a Random Projection Squashing step to ensure that complexity increases only linearly. To achieve low information loss, we introduce a Relation-wise Neighbor Collection component with an Even-odd Propagation Scheme, which aims to collect information from neighbors in a finer-grained way. Experimental results indicate that our approach achieves state-of-the-art results on seven small and large benchmark datasets while also being 230% faster compared to the most effective baseline. Surprisingly, our approach not only surpasses pre-processing-based baselines but also outperforms end-to-end methods.
Graph Neural Networks (GNNs) have evolved to understand graph structures through recursive exchanges and aggregations among nodes. To enhance robustness, self-supervised learning (SSL) has become a vital tool for data augmentation. Traditional methods often depend on fine-tuning with task-specific labels, limiting their effectiveness when labeled data is scarce. Our research tackles this by advancing graph model generalization in zero-shot learning environments. Inspired by the success of large language models (LLMs), we aim to create a graph-oriented LLM capable of exceptional generalization across various datasets and tasks without relying on downstream graph data. We introduce the GraphGPT framework, which integrates LLMs with graph structural knowledge through graph instruction tuning. This framework includes a text-graph grounding component to link textual and graph structures and a dual-stage instruction tuning approach with a lightweight graph-text alignment projector. These innovations allow LLMs to comprehend complex graph structures and enhance adaptability across diverse datasets and tasks. Our framework demonstrates superior generalization in both supervised and zero-shot graph learning tasks, surpassing existing benchmarks. The open-sourced model implementation of our GraphGPT is available at https://github.com/HKUDS/GraphGPT.
We study the problem of lifelong graph learning in an open-world scenario, where a model needs to deal with new tasks and potentially unknown classes. We utilize Out-of-Distribution (OOD) detection methods to recognize new classes and adapt existing non-graph OOD detection methods to graph data. Crucially, we suggest performing new class detection by combining OOD detection methods with information aggregated from the graph neighborhood. Most OOD detection methods avoid determining a crisp threshold for deciding whether a vertex is OOD. To tackle this problem, we propose a Weakly-supervised Relevance Feedback (Open-WRF) method, which decreases the sensitivity to thresholds in OOD detection. We evaluate our approach on six benchmark datasets. Our results show that the proposed neighborhood aggregation method for OOD scores outperforms existing methods independent of the underlying graph neural network. Furthermore, we demonstrate that our Open-WRF method is more robust to threshold selection and analyze the influence of graph neighborhood on OOD detection. The aggregation and threshold methods are compatible with arbitrary graph neural networks and OOD detection methods, making our approach versatile and applicable to many real-world applications.
Graph Neural Networks (GNNs) have been widely used for various types of graph data processing and analytical tasks in different domains. Training GNNs over centralized graph data can be infeasible due to privacy concerns and regulatory restrictions. Thus, federated learning (FL) becomes a trending solution to address this challenge in a distributed learning paradigm. However, as GNNs may inherit historical bias from training data and lead to discriminatory predictions, the bias of local models can be easily propagated to the global model in distributed settings. This poses a new challenge in mitigating bias in federated GNNs. To address this challenge, we propose $\text{F}^2$GNN, a Fair Federated Graph Neural Network, that enhances group fairness of federated GNNs. As bias can be sourced from both data and learning algorithms, $\text{F}^2$GNN aims to mitigate both types of bias under federated settings. First, we provide theoretical insights on the connection between data bias in a training graph and statistical fairness metrics of the trained GNN models. Based on the theoretical analysis, we design $\text{F}^2$GNN which contains two key components: a fairness-aware local model update scheme that enhances group fairness of the local models on the client side, and a fairness-weighted global model update scheme that takes both data bias and fairness metrics of local models into consideration in the aggregation process. We evaluate $\text{F}^2$GNN empirically versus a number of baseline methods, and demonstrate that $\text{F}^2$GNN outperforms these baselines in terms of both fairness and model accuracy.
Graph neural networks (GNNs) have gained prominence in recommendation systems in recent years. By representing the user-item matrix as a bipartite and undirected graph, GNNs have demonstrated their potential to capture short- and long-distance user-item interactions, thereby learning more accurate preference patterns than traditional recommendation approaches. In contrast to previous tutorials on the same topic, this tutorial aims to present and examine three key aspects that characterize GNNs for recommendation: (i) the reproducibility of state-of-the-art approaches, (ii) the potential impact of graph topological characteristics on the performance of these models, and (iii) strategies for learning node representations when training features from scratch or utilizing pre-trained embeddings as additional item information (e.g., multimodal features). The goal is to provide three novel theoretical and practical perspectives on the field, currently subject to debate in graph learning but long been overlooked in the context of recommendation systems.
Text-attributed graphs have recently garnered significant attention due to their wide range of applications in web domains. Existing methodologies employ word embedding models for acquiring text representations as node features, which are subsequently fed into Graph Neural Networks (GNNs) for training. Recently, the advent of Large Language Models (LLMs) has introduced their powerful capabilities in information retrieval and text generation, which can greatly enhance the text attributes of graph data. Furthermore, the acquisition and labeling of extensive datasets are both costly and time-consuming endeavors. Consequently, few-shot learning has emerged as a crucial problem in the context of graph learning tasks. In order to tackle this challenge, we propose a lightweight paradigm called LLM4NG, which adopts a plug-and-play approach to empower text-attributed graphs through node generation using LLMs. Specifically, we utilize LLMs to extract semantic information from the labels and generate samples that belong to these categories as exemplars. Subsequently, we employ an edge predictor to capture the structural information inherent in the raw dataset and integrate the newly generated samples into the original graph. This approach harnesses LLMs for enhancing class-level information and seamlessly introduces labeled nodes and edges without modifying the raw dataset, thereby facilitating the node classification task in few-shot scenarios. Extensive experiments demonstrate the outstanding performance of our proposed paradigm, particularly in low-shot scenarios. For instance, in the 1-shot setting of the ogbn-arxiv dataset, LLM4NG achieves a 76% improvement over the baseline model.