Federated graph learning is an emerging field with significant practical challenges. While algorithms have been proposed to improve the accuracy of training graph neural networks, such as node classification on federated graphs, the system performance is often overlooked, despite it is crucial for real-world deployment. To bridge this gap, we introduce FedGraph, a research library designed for practical distributed training and comprehensive benchmarking of FGL algorithms. FedGraph supports a range of state-of-the-art graph learning methods and includes a monitoring class that evaluates system performance, with a particular focus on communication and computation costs during training. Unlike existing federated learning platforms, FedGraph natively integrates homomorphic encryption to enhance privacy preservation and supports scalable deployment across multiple physical machines with system-level performance evaluation to guide the system design of future algorithms. To enhance efficiency and privacy, we propose a low-rank communication scheme for algorithms like FedGCN that require pre-training communication, accelerating both the pre-training and training phases. Extensive experiments benchmark different FGL algorithms on three major graph learning tasks and demonstrate FedGraph as the first efficient FGL framework to support encrypted low-rank communication and scale to graphs with 100 million nodes.
In the realm of graph learning, there is a category of methods that conceptualize graphs as hierarchical structures, utilizing node clustering to capture broader structural information. While generally effective, these methods often rely on a fixed graph coarsening routine, leading to overly homogeneous cluster representations and loss of node-level information. In this paper, we envision the graph as a network of interconnected node sets without compressing each cluster into a single embedding. To enable effective information transfer among these node sets, we propose the Node-to-Cluster Attention (N2C-Attn) mechanism. N2C-Attn incorporates techniques from Multiple Kernel Learning into the kernelized attention framework, effectively capturing information at both node and cluster levels. We then devise an efficient form for N2C-Attn using the cluster-wise message-passing framework, achieving linear time complexity. We further analyze how N2C-Attn combines bi-level feature maps of queries and keys, demonstrating its capability to merge dual-granularity information. The resulting architecture, Cluster-wise Graph Transformer (Cluster-GT), which uses node clusters as tokens and employs our proposed N2C-Attn module, shows superior performance on various graph-level tasks. Code is available at https://github.com/LUMIA-Group/Cluster-wise-Graph-Transformer.
Attention mechanisms have made significant strides in graph learning, yet they still exhibit notable limitations: local attention faces challenges in capturing long-range information due to the inherent problems of the message-passing scheme, while global attention cannot reflect the hierarchical neighborhood structure and fails to capture fine-grained local information. In this paper, we propose a novel multi-hop graph attention mechanism, named Subtree Attention (STA), to address the aforementioned issues. STA seamlessly bridges the fully-attentional structure and the rooted subtree, with theoretical proof that STA approximates the global attention under extreme settings. By allowing direct computation of attention weights among multi-hop neighbors, STA mitigates the inherent problems in existing graph attention mechanisms. Further we devise an efficient form for STA by employing kernelized softmax, which yields a linear time complexity. Our resulting GNN architecture, the STAGNN, presents a simple yet performant STA-based graph neural network leveraging a hop-aware attention strategy. Comprehensive evaluations on ten node classification datasets demonstrate that STA-based models outperform existing graph transformers and mainstream GNNs. The code is available at https://github.com/LUMIA-Group/SubTree-Attention.
Identifying unusual brain activity is a crucial task in neuroscience research, as it aids in the early detection of brain disorders. It is common to represent brain networks as graphs, and researchers have developed various graph-based machine learning methods for analyzing them. However, the majority of existing graph learning tools for the brain face a combination of the following three key limitations. First, they focus only on pairwise correlations between regions of the brain, limiting their ability to capture synchronized activity among larger groups of regions. Second, they model the brain network as a static network, overlooking the temporal changes in the brain. Third, most are designed only for classifying brain networks as healthy or disordered, lacking the ability to identify abnormal brain activity patterns linked to biomarkers associated with disorders. To address these issues, we present HyperBrain, an unsupervised anomaly detection framework for temporal hypergraph brain networks. HyperBrain models fMRI time series data as temporal hypergraphs capturing dynamic higher-order interactions. It then uses a novel customized temporal walk (BrainWalk) and neural encodings to detect abnormal co-activations among brain regions. We evaluate the performance of HyperBrain in both synthetic and real-world settings for Autism Spectrum Disorder and Attention Deficit Hyperactivity Disorder(ADHD). HyperBrain outperforms all other baselines on detecting abnormal co-activations in brain networks. Furthermore, results obtained from HyperBrain are consistent with clinical research on these brain disorders. Our findings suggest that learning temporal and higher-order connections in the brain provides a promising approach to uncover intricate connectivity patterns in brain networks, offering improved diagnosis.
Understanding how neuronal networks reorganize in response to external stimuli and give rise to behavior is a central challenge in neuroscience and artificial intelligence. However, existing methods often fail to capture the evolving structure of neural connectivity in ways that capture its relationship to behavior, especially in dynamic, uncertain, or high-dimensional settings with sufficient resolution or interpretability. We introduce the Temporal Attention-enhanced Variational Graph Recurrent Neural Network (TAVRNN), a novel framework that models time-varying neuronal connectivity by integrating probabilistic graph learning with temporal attention mechanisms. TAVRNN learns latent dynamics at the single-unit level while maintaining interpretable population-level representations, to identify key connectivity patterns linked to behavior. TAVRNN generalizes across diverse neural systems and modalities, demonstrating state-of-the-art classification and clustering performance. We validate TAVRNN on three diverse datasets: (1) electrophysiological data from a freely behaving rat, (2) primate somatosensory cortex recordings during a reaching task, and (3) biological neurons in the DishBrain platform interacting with a virtual game environment. Our method outperforms state-of-the-art dynamic embedding techniques, revealing previously unreported relationships between adaptive behavior and the evolving topological organization of neural networks. These findings demonstrate that TAVRNN offers a powerful and generalizable approach for modeling neural dynamics across experimental and synthetic biological systems. Its architecture is modality-agnostic and scalable, making it applicable across a wide range of neural recording platforms and behavioral paradigms.
Human Activity Recognition (HAR) is a challenging, multi-label classification problem as activities may co-occur and sensor signals corresponding to the same activity may vary in different contexts (e.g., different device placements). This paper proposes a Deep Heterogeneous Contrastive Hyper-Graph Learning (DHC-HGL) framework that captures heterogenous Context-Aware HAR (CA-HAR) hypergraph properties in a message-passing and neighborhood-aggregation fashion. Prior work only explored homogeneous or shallow-node-heterogeneous graphs. DHC-HGL handles heterogeneous CA-HAR data by innovatively 1) Constructing three different types of sub-hypergraphs that are each passed through different custom HyperGraph Convolution (HGC) layers designed to handle edge-heterogeneity and 2) Adopting a contrastive loss function to ensure node-heterogeneity. In rigorous evaluation on two CA-HAR datasets, DHC-HGL significantly outperformed state-of-the-art baselines by 5.8% to 16.7% on Matthews Correlation Coefficient (MCC) and 3.0% to 8.4% on Macro F1 scores. UMAP visualizations of learned CA-HAR node embeddings are also presented to enhance model explainability.
Unsupervised Multiplex Graph Learning (UMGL) aims to learn node representations on various edge types without manual labeling. However, existing research overlooks a key factor: the reliability of the graph structure. Real-world data often exhibit a complex nature and contain abundant task-irrelevant noise, severely compromising UMGL's performance. Moreover, existing methods primarily rely on contrastive learning to maximize mutual information across different graphs, limiting them to multiplex graph redundant scenarios and failing to capture view-unique task-relevant information. In this paper, we focus on a more realistic and challenging task: to unsupervisedly learn a fused graph from multiple graphs that preserve sufficient task-relevant information while removing task-irrelevant noise. Specifically, our proposed Information-aware Unsupervised Multiplex Graph Fusion framework (InfoMGF) uses graph structure refinement to eliminate irrelevant noise and simultaneously maximizes view-shared and view-unique task-relevant information, thereby tackling the frontier of non-redundant multiplex graph. Theoretical analyses further guarantee the effectiveness of InfoMGF. Comprehensive experiments against various baselines on different downstream tasks demonstrate its superior performance and robustness. Surprisingly, our unsupervised method even beats the sophisticated supervised approaches. The source code and datasets are available at https://github.com/zxlearningdeep/InfoMGF.
Capitalizing on the intuitive premise that shape characteristics are more robust to perturbations, we bridge adversarial graph learning with the emerging tools from computational topology, namely, persistent homology representations of graphs. We introduce the concept of witness complex to adversarial analysis on graphs, which allows us to focus only on the salient shape characteristics of graphs, yielded by the subset of the most essential nodes (i.e., landmarks), with minimal loss of topological information on the whole graph. The remaining nodes are then used as witnesses, governing which higher-order graph substructures are incorporated into the learning process. Armed with the witness mechanism, we design Witness Graph Topological Layer (WGTL), which systematically integrates both local and global topological graph feature representations, the impact of which is, in turn, automatically controlled by the robust regularized topological loss. Given the attacker's budget, we derive the important stability guarantees of both local and global topology encodings and the associated robust topological loss. We illustrate the versatility and efficiency of WGTL by its integration with five GNNs and three existing non-topological defense mechanisms. Our extensive experiments across six datasets demonstrate that WGTL boosts the robustness of GNNs across a range of perturbations and against a range of adversarial attacks, leading to relative gains of up to 18%.
With the prosperity of contrastive learning for visual representation learning (VCL), it is also adapted to the graph domain and yields promising performance. However, through a systematic study of various graph contrastive learning (GCL) methods, we observe that some common phenomena among existing GCL methods that are quite different from the original VCL methods, including 1) positive samples are not a must for GCL; 2) negative samples are not necessary for graph classification, neither for node classification when adopting specific normalization modules; 3) data augmentations have much less influence on GCL, as simple domain-agnostic augmentations (e.g., Gaussian noise) can also attain fairly good performance. By uncovering how the implicit inductive bias of GNNs works in contrastive learning, we theoretically provide insights into the above intriguing properties of GCL. Rather than directly porting existing VCL methods to GCL, we advocate for more attention toward the unique architecture of graph learning and consider its implicit influence when designing GCL methods. Code is available at https: //github.com/PKU-ML/ArchitectureMattersGCL.
This paper addresses the problem of online network topology inference for expanding graphs from a stream of spatiotemporal signals. Online algorithms for dynamic graph learning are crucial in delay-sensitive applications or when changes in topology occur rapidly. While existing works focus on inferring the connectivity within a fixed set of nodes, in practice, the graph can grow as new nodes join the network. This poses additional challenges like modeling temporal dynamics involving signals and graphs of different sizes. This growth also increases the computational complexity of the learning process, which may become prohibitive. To the best of our knowledge, this is the first work to tackle this setting. We propose a general online algorithm based on projected proximal gradient descent that accounts for the increasing graph size at each iteration. Recursively updating the sample covariance matrix is a key aspect of our approach. We introduce a strategy that enables different types of updates for nodes that just joined the network and for previously existing nodes. To provide further insights into the proposed method, we specialize it in Gaussian Markov random field settings, where we analyze the computational complexity and characterize the dynamic cumulative regret. Finally, we demonstrate the effectiveness of the proposed approach using both controlled experiments and real-world datasets from epidemic and financial networks.
Graph neural networks have become the default choice by practitioners for graph learning tasks such as graph classification and node classification. Nevertheless, popular graph neural network models still struggle to capture higher-order information, i.e., information that goes \emph{beyond} pairwise interactions. Recent work has shown that persistent homology, a tool from topological data analysis, can enrich graph neural networks with topological information that they otherwise could not capture. Calculating such features is efficient for dimension 0 (connected components) and dimension 1 (cycles). However, when it comes to higher-order structures, it does not scale well, with a complexity of $O(n^d)$, where $n$ is the number of nodes and $d$ is the order of the structures. In this work, we introduce a novel method that extracts information about higher-order structures in the graph while still using the efficient low-dimensional persistent homology algorithm. On standard benchmark datasets, we show that our method can lead to up to $31\%$ improvements in test accuracy.
Graph partitioning (GP) is a classic problem that divides the node set of a graph into densely-connected blocks. Following the IEEE HPEC Graph Challenge and recent advances in pre-training techniques (e.g., large-language models), we propose PR-GPT (Pre-trained & Refined Graph ParTitioning) based on a novel pre-training & refinement paradigm. We first conduct the offline pre-training of a deep graph learning (DGL) model on small synthetic graphs with various topology properties. By using the inductive inference of DGL, one can directly generalize the pre-trained model (with frozen model parameters) to large graphs and derive feasible GP results. We also use the derived partition as a good initialization of an efficient GP method (e.g., InfoMap) to further refine the quality of partitioning. In this setting, the online generalization and refinement of PR-GPT can not only benefit from the transfer ability regarding quality but also ensure high inference efficiency without re-training. Based on a mechanism of reducing the scale of a graph to be processed by the refinement method, PR-GPT also has the potential to support streaming GP. Experiments on the Graph Challenge benchmark demonstrate that PR-GPT can ensure faster GP on large-scale graphs without significant quality degradation, compared with running a refinement method from scratch. We will make our code public at https://github.com/KuroginQin/PRGPT.
Federated graph learning (FGL) is a promising distributed training paradigm for graph neural networks across multiple local systems without direct data sharing. This approach inherently involves large-scale distributed graph processing, which closely aligns with the challenges and research focuses of graph-based data systems. Despite the proliferation of FGL, the diverse motivations from real-world applications, spanning various research backgrounds and settings, pose a significant challenge to fair evaluation. To fill this gap, we propose OpenFGL, a unified benchmark designed for the primary FGL scenarios: Graph-FL and Subgraph-FL. Specifically, OpenFGL includes 42 graph datasets from 18 application domains, 8 federated data simulation strategies that emphasize different graph properties, and 5 graph-based downstream tasks. Additionally, it offers 18 recently proposed SOTA FGL algorithms through a user-friendly API, enabling a thorough comparison and comprehensive evaluation of their effectiveness, robustness, and efficiency. Our empirical results demonstrate the capabilities of FGL while also highlighting its potential limitations, providing valuable insights for future research in this growing field, particularly in fostering greater interdisciplinary collaboration between FGL and data systems.
The growing ubiquity of relational data structured as graphs has underscored the need for graph learning models with exceptional generalization capabilities. However, current approaches often struggle to effectively extract generalizable insights, frequently requiring extensive fine-tuning and limiting their versatility. Graph foundation models offer a transformative solution, with the potential to learn robust, generalizable representations from graph data. This enables more effective and adaptable applications across a wide spectrum of tasks and domains. In this work, we investigate a unified graph model, AnyGraph, designed to handle key challenges: i) Structure Heterogenity. Addressing distribution shift in graph structural information; ii) Feature Heterogenity. Handling diverse feature representation spaces across graph datasets; iii) Fast Adaptation. Efficiently adapting the model to new graph domains; iv) Scaling Law Emergence. Enabling the model to exhibit scaling law behavior, where its performance scales favorably with the amount of data and parameter sizes. To tackle these critical challenges, we build the AnyGraph upon a Graph Mixture-of-Experts (MoE) architecture. This approach empowers the model to effectively manage both the in-domain and cross-domain distribution shift concerning structure-level and feature-level heterogeneity. Furthermore, a lightweight graph expert routing mechanism is proposed to facilitate AnyGraph's fast adaptability to new data and domains. Our extensive experiments on diverse 38 graph datasets have demonstrated the strong zero-shot learning performance of AnyGraph across diverse graph domains with significant distribution shift. Furthermore, we have validated the model's fast adaptation ability and scaling law emergence, showcasing its versatility.
Federated Graph Learning (FGL) aims to learn graph learning models over graph data distributed in multiple data owners, which has been applied in various applications such as social recommendation and financial fraud detection. Inherited from generic Federated Learning (FL), FGL similarly has the data heterogeneity issue where the label distribution may vary significantly for distributed graph data across clients. For instance, a client can have the majority of nodes from a class, while another client may have only a few nodes from the same class. This issue results in divergent local objectives and impairs FGL convergence for node-level tasks, especially for node classification. Moreover, FGL also encounters a unique challenge for the node classification task: the nodes from a minority class in a client are more likely to have biased neighboring information, which prevents FGL from learning expressive node embeddings with Graph Neural Networks (GNNs). To grapple with the challenge, we propose FedSpray, a novel FGL framework that learns local class-wise structure proxies in the latent space and aligns them to obtain global structure proxies in the server. Our goal is to obtain the aligned structure proxies that can serve as reliable, unbiased neighboring information for node classification. To achieve this, FedSpray trains a global feature-structure encoder and generates unbiased soft targets with structure proxies to regularize local training of GNN models in a personalized way. We conduct extensive experiments over four datasets, and experiment results validate the superiority of FedSpray compared with other baselines. Our code is available at https://github.com/xbfu/FedSpray.
Continual learning has emerged as a crucial paradigm for learning from sequential data while preserving previous knowledge. In the realm of continual graph learning, where graphs continuously evolve based on streaming graph data, continual graph learning presents unique challenges that require adaptive and efficient graph learning methods in addition to the problem of catastrophic forgetting. The first challenge arises from the interdependencies between different graph data, where previous graphs can influence new data distributions. The second challenge lies in the efficiency concern when dealing with large graphs. To addresses these two problems, we produce an Efficient Continual Graph Learner (E-CGL) in this paper. We tackle the interdependencies issue by demonstrating the effectiveness of replay strategies and introducing a combined sampling strategy that considers both node importance and diversity. To overcome the limitation of efficiency, E-CGL leverages a simple yet effective MLP model that shares weights with a GCN during training, achieving acceleration by circumventing the computationally expensive message passing process. Our method comprehensively surpasses nine baselines on four graph continual learning datasets under two settings, meanwhile E-CGL largely reduces the catastrophic forgetting problem down to an average of -1.1%. Additionally, E-CGL achieves an average of 15.83x training time acceleration and 4.89x inference time acceleration across the four datasets. These results indicate that E-CGL not only effectively manages the correlation between different graph data during continual training but also enhances the efficiency of continual learning on large graphs. The code is publicly available at https://github.com/aubreygjh/E-CGL.
In the fields of computer vision and robotics, accurate pixel-level correspondences are essential for enabling advanced tasks such as structure-from-motion and simultaneous localization and mapping. Recent correspondence pruning methods usually focus on learning local consistency through k-nearest neighbors, which makes it difficult to capture robust context for each correspondence. We propose CorrAdaptor, a novel architecture that introduces a dual-branch structure capable of adaptively adjusting local contexts through both explicit and implicit local graph learning. Specifically, the explicit branch uses KNN-based graphs tailored for initial neighborhood identification, while the implicit branch leverages a learnable matrix to softly assign neighbors and adaptively expand the local context scope, significantly enhancing the model's robustness and adaptability to complex image variations. Moreover, we design a motion injection module to integrate motion consistency into the network to suppress the impact of outliers and refine local context learning, resulting in substantial performance improvements. The experimental results on extensive correspondence-based tasks indicate that our CorrAdaptor achieves state-of-the-art performance both qualitatively and quantitatively. The code and pre-trained models are available at https://github.com/TaoWangzj/CorrAdaptor.
When learning from graph data, the graph and the node features both give noisy information about the node labels. In this paper we propose an algorithm to jointly denoise the features and rewire the graph (JDR), which improves the performance of downstream node classification graph neural nets (GNNs). JDR works by aligning the leading spectral spaces of graph and feature matrices. It approximately solves the associated non-convex optimization problem in a way that handles graphs with multiple classes and different levels of homophily or heterophily. We theoretically justify JDR in a stylized setting and show that it consistently outperforms existing rewiring methods on a wide range of synthetic and real-world node classification tasks.
Learning electronic health records (EHRs) has received emerging attention because of its capability to facilitate accurate medical diagnosis. Since the EHRs contain enriched information specifying complex interactions between entities, modeling EHRs with graphs is shown to be effective in practice. The EHRs, however, present a great degree of heterogeneity, sparsity, and complexity, which hamper the performance of most of the models applied to them. Moreover, existing approaches modeling EHRs often focus on learning the representations for a single task, overlooking the multi-task nature of EHR analysis problems and resulting in limited generalizability across different tasks. In view of these limitations, we propose a novel framework for EHR modeling, namely MulT-EHR (Multi-Task EHR), which leverages a heterogeneous graph to mine the complex relations and model the heterogeneity in the EHRs. To mitigate the large degree of noise, we introduce a denoising module based on the causal inference framework to adjust for severe confounding effects and reduce noise in the EHR data. Additionally, since our model adopts a single graph neural network for simultaneous multi-task prediction, we design a multi-task learning module to leverage the inter-task knowledge to regularize the training process. Extensive empirical studies on MIMIC-III and MIMIC-IV datasets validate that the proposed method consistently outperforms the state-of-the-art designs in four popular EHR analysis tasks -- drug recommendation, and predictions of the length of stay, mortality, and readmission. Thorough ablation studies demonstrate the robustness of our method upon variations to key components and hyperparameters.
Graph Neural Networks (GNNs) are important across different domains, such as social network analysis and recommendation systems, due to their ability to model complex relational data. This paper introduces subgraph queries as a new task for deep graph learning. Unlike traditional graph prediction tasks that focus on individual components like link prediction or node classification, subgraph queries jointly predict the components of a target subgraph based on evidence that is represented by an observed subgraph. For instance, a subgraph query can predict a set of target links and/or node labels. To answer subgraph queries, we utilize a probabilistic deep Graph Generative Model. Specifically, we inductively train a Variational Graph Auto-Encoder (VGAE) model, augmented to represent a joint distribution over links, node features and labels. Bayesian optimization is used to tune a weighting for the relative importance of links, node features and labels in a specific domain. We describe a deterministic and a sampling-based inference method for estimating subgraph probabilities from the VGAE generative graph distribution, without retraining, in zero-shot fashion. For evaluation, we apply the inference methods on a range of subgraph queries on six benchmark datasets. We find that inference from a model achieves superior predictive performance, surpassing independent prediction baselines with improvements in AUC scores ranging from 0.06 to 0.2 points, depending on the dataset.