The insufficient supervision limit the performance of the deep supervised models for brain disease diagnosis. It is important to develop a learning framework that can capture more information in limited data and insufficient supervision. To address these issues at some extend, we propose a multi-stage graph learning framework which incorporates 1) pretrain stage : self-supervised graph learning on insufficient supervision of the fmri data 2) fine-tune stage : supervised graph learning for brain disorder diagnosis. Experiment results on three datasets, Autism Brain Imaging Data Exchange ABIDE I, ABIDE II and ADHD with AAL1,demonstrating the superiority and generalizability of the proposed framework compared to the state of art of models.(ranging from 0.7330 to 0.9321,0.7209 to 0.9021,0.6338 to 0.6699)
Graph self-supervised learning (GSSL) has emerged as a compelling framework for extracting informative representations from graph-structured data without extensive reliance on labeled inputs. In this study, we introduce Graph Interplay (GIP), an innovative and versatile approach that significantly enhances the performance equipped with various existing GSSL methods. To this end, GIP advocates direct graph-level communications by introducing random inter-graph edges within standard batches. Against GIP's simplicity, we further theoretically show that \textsc{GIP} essentially performs a principled manifold separation via combining inter-graph message passing and GSSL, bringing about more structured embedding manifolds and thus benefits a series of downstream tasks. Our empirical study demonstrates that GIP surpasses the performance of prevailing GSSL methods across multiple benchmarks by significant margins, highlighting its potential as a breakthrough approach. Besides, GIP can be readily integrated into a series of GSSL methods and consistently offers additional performance gain. This advancement not only amplifies the capability of GSSL but also potentially sets the stage for a novel graph learning paradigm in a broader sense.
With the trend of large graph learning models, business owners tend to employ a model provided by a third party to deliver business services to users. However, these models might be backdoored, and malicious users can submit trigger-embedded inputs to manipulate the model predictions. Current graph backdoor defenses have several limitations: 1) depending on model-related details, 2) requiring additional model fine-tuning, and 3) relying upon extra explainability tools, all of which are infeasible under stringent privacy policies. To address those limitations, we propose GraphProt, which allows resource-constrained business owners to rely on third parties to avoid backdoor attacks on GNN-based graph classifiers. Our GraphProt is model-agnostic and only relies on the input graph. The key insight is to leverage subgraph information for prediction, thereby mitigating backdoor effects induced by triggers. GraphProt comprises two components: clustering-based trigger elimination and robust subgraph ensemble. Specifically, we first propose feature-topology clustering that aims to remove most of the anomalous subgraphs (triggers). Moreover, we design subgraph sampling strategies based on feature-topology clustering to build a robust classifier via majority vote. Experimental results across three backdoor attacks and six benchmark datasets demonstrate that GraphProt significantly reduces the backdoor attack success rate while preserving the model accuracy on regular graph classification tasks.
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.
With the increasing prevalence of graph-structured data, multi-view graph clustering has been widely used in various downstream applications. Existing approaches primarily rely on a unified message passing mechanism, which significantly enhances clustering performance. Nevertheless, this mechanism limits its applicability to heterophilous situations, as it is fundamentally predicated on the assumption of homophily, i.e., the connected nodes often belong to the same class. In reality, this assumption does not always hold; a moderately or even mildly homophilous graph is more common than a fully homophilous one due to inevitable heterophilous information in the graph. To address this issue, in this paper, we propose a novel SiMilarity-enhanced Homophily for Multi-view Heterophilous Graph Clustering (SMHGC) approach. By analyzing the relationship between similarity and graph homophily, we propose to enhance the homophily by introducing three similarity terms, i.e., neighbor pattern similarity, node feature similarity, and multi-view global similarity, in a label-free manner. Then, a consensus-based inter- and intra-view fusion paradigm is proposed to fuse the improved homophilous graph from different views and utilize them for clustering. The state-of-the-art experimental results on both multi-view heterophilous and homophilous datasets collectively demonstrate the strong capacity of similarity for unsupervised multi-view heterophilous graph learning. Additionally, the consistent performance across semi-synthetic datasets with varying levels of homophily serves as further evidence of SMHGC's resilience to heterophily.
Language Models (LMs) are increasingly challenging the dominance of domain-specific models, such as Graph Neural Networks (GNNs) and Graph Transformers (GTs), in graph learning tasks. Following this trend, we propose a novel approach that empowers off-the-shelf LMs to achieve performance comparable to state-of-the-art (SOTA) GNNs on node classification tasks, without requiring any architectural modification. By preserving the LM's original architecture, our approach retains a key benefit of LM instruction tuning: the ability to jointly train on diverse datasets, fostering greater flexibility and efficiency. To achieve this, we introduce two key augmentation strategies: (1) Enriching LMs' input using topological and semantic retrieval methods, which provide richer contextual information, and (2) guiding the LMs' classification process through a lightweight GNN classifier that effectively prunes class candidates. Our experiments on real-world datasets show that backbone Flan-T5 LMs equipped with these augmentation strategies outperform SOTA text-output node classifiers and are comparable to top-performing vector-output node classifiers. By bridging the gap between specialized node classifiers and general LMs, this work paves the way for more versatile and widely applicable graph learning models. We will open-source the code upon publication.
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.
Solving partial differential equations (PDEs) serves as a cornerstone for modeling complex dynamical systems. Recent progresses have demonstrated grand benefits of data-driven neural-based models for predicting spatiotemporal dynamics (e.g., tremendous speedup gain compared with classical numerical methods). However, most existing neural models rely on rich training data, have limited extrapolation and generalization abilities, and suffer to produce precise or reliable physical prediction under intricate conditions (e.g., irregular mesh or geometry, complex boundary conditions, diverse PDE parameters, etc.). To this end, we propose a new graph learning approach, namely, Physics-encoded Message Passing Graph Network (PhyMPGN), to model spatiotemporal PDE systems on irregular meshes given small training datasets. Specifically, we incorporate a GNN into a numerical integrator to approximate the temporal marching of spatiotemporal dynamics for a given PDE system. Considering that many physical phenomena are governed by diffusion processes, we further design a learnable Laplace block, which encodes the discrete Laplace-Beltrami operator, to aid and guide the GNN learning in a physically feasible solution space. A boundary condition padding strategy is also designed to improve the model convergence and accuracy. Extensive experiments demonstrate that PhyMPGN is capable of accurately predicting various types of spatiotemporal dynamics on coarse unstructured meshes, consistently achieves the state-of-the-art results, and outperforms other baselines with considerable gains.
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.
Labor market forecasting on talent demand and supply is essential for business management and economic development. With accurate and timely forecasts, employers can adapt their recruitment strategies to align with the evolving labor market, and employees can have proactive career path planning according to future demand and supply. However, previous studies ignore the interconnection between demand-supply sequences among different companies and positions for predicting variations. Moreover, companies are reluctant to share their private human resource data for global labor market analysis due to concerns over jeopardizing competitive advantage, security threats, and potential ethical or legal violations. To this end, in this paper, we formulate the Federated Labor Market Forecasting (FedLMF) problem and propose a Meta-personalized Convergence-aware Clustered Federated Learning (MPCAC-FL) framework to provide accurate and timely collaborative talent demand and supply prediction in a privacy-preserving way. First, we design a graph-based sequential model to capture the inherent correlation between demand and supply sequences and company-position pairs. Second, we adopt meta-learning techniques to learn effective initial model parameters that can be shared across companies, allowing personalized models to be optimized for forecasting company-specific demand and supply, even when companies have heterogeneous data. Third, we devise a Convergence-aware Clustering algorithm to dynamically divide companies into groups according to model similarity and apply federated aggregation in each group. The heterogeneity can be alleviated for more stable convergence and better performance. Extensive experiments demonstrate that MPCAC-FL outperforms compared baselines on three real-world datasets and achieves over 97% of the state-of-the-art model, i.e., DH-GEM, without exposing private company data.
Graph Neural Networks (GNNs) training often necessitates gathering raw user data on a central server, which raises significant privacy concerns. Federated learning emerges as a solution, enabling collaborative model training without users directly sharing their raw data. However, integrating federated learning with GNNs presents unique challenges, especially when a client represents a graph node and holds merely a single feature vector. In this paper, we propose a novel framework for node-level federated graph learning. Specifically, we decouple the message-passing and feature vector transformation processes of the first GNN layer, allowing them to be executed separately on the user devices and the cloud server. Moreover, we introduce a graph Laplacian term based on the feature vector's latent representation to regulate the user-side model updates. The experiment results on multiple datasets show that our approach achieves better performance compared with baselines.
Large Language Models (LLMs) have achieved impressive results in processing text data, which has sparked interest in applying these models beyond textual data, such as graphs. In the field of graph learning, there is a growing interest in harnessing LLMs to comprehend and manipulate graph-structured data. Existing research predominantly focuses on graphs with rich textual features, such as knowledge graphs or text attribute graphs, leveraging LLMs' ability to process text but inadequately addressing graph structure. This work specifically aims to assess and enhance LLMs' abilities to comprehend and utilize the structural knowledge inherent in graph data itself, rather than focusing solely on graphs rich in textual content. To achieve this, we introduce the \textbf{G}raph \textbf{U}nderstanding for \textbf{N}atural Language \textbf{D}riven \textbf{A}nalytical \textbf{M}odel (\model). This model adapts LLMs to better understand and engage with the structure of graph data, enabling them to perform complex reasoning tasks by leveraging the graph's structure itself. Our experimental evaluations on graph reasoning benchmarks not only substantiate that \model~ outperforms the SOTA baselines for comparisons. But also reveals key factors affecting the graph reasoning capabilities of LLMs. Moreover, we provide a theoretical analysis illustrating how reasoning paths can enhance LLMs' reasoning capabilities.
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.
Heterophily, or the tendency of connected nodes in networks to have different class labels or dissimilar features, has been identified as challenging for many Graph Neural Network (GNN) models. While the challenges of applying GNNs for node classification when class labels display strong heterophily are well understood, it is unclear how heterophily affects GNN performance in other important graph learning tasks where class labels are not available. In this work, we focus on the link prediction task and systematically analyze the impact of heterophily in node features on GNN performance. Theoretically, we first introduce formal definitions of homophilic and heterophilic link prediction tasks, and present a theoretical framework that highlights the different optimizations needed for the respective tasks. We then analyze how different link prediction encoders and decoders adapt to varying levels of feature homophily and introduce designs for improved performance. Our empirical analysis on a variety of synthetic and real-world datasets confirms our theoretical insights and highlights the importance of adopting learnable decoders and GNN encoders with ego- and neighbor-embedding separation in message passing for link prediction tasks beyond homophily.
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.
Hydrometric forecasting is crucial for managing water resources, flood prediction, and environmental protection. Water stations are interconnected, and this connectivity influences the measurements at other stations. However, the dynamic and implicit nature of water flow paths makes it challenging to extract a priori knowledge of the connectivity structure. We hypothesize that terrain elevation significantly affects flow and connectivity. To incorporate this, we use LiDAR terrain elevation data encoded through a Vision Transformer (ViT). The ViT, which has demonstrated excellent performance in image classification by directly applying transformers to sequences of image patches, efficiently captures spatial features of terrain elevation. To account for both spatial and temporal features, we employ GRU blocks enhanced with graph convolution, a method widely used in the literature. We propose a hybrid graph learning structure that combines static and dynamic graph learning. A static graph, derived from transformer-encoded LiDAR data, captures terrain elevation relationships, while a dynamic graph adapts to temporal changes, improving the overall graph representation. We apply graph convolution in two layers through these static and dynamic graphs. Our method makes daily predictions up to 12 days ahead. Empirical results from multiple water stations in Quebec demonstrate that our method significantly reduces prediction error by an average of 10\% across all days, with greater improvements for longer forecasting horizons.
For privacy-preserving graph learning tasks involving distributed graph datasets, federated learning (FL)-based GCN (FedGCN) training is required. A key challenge for FedGCN is scaling to large-scale graphs, which typically incurs high computation and communication costs when dealing with the explosively increasing number of neighbors. Existing graph sampling-enhanced FedGCN training approaches ignore graph structural information or dynamics of optimization, resulting in high variance and inaccurate node embeddings. To address this limitation, we propose the Federated Adaptive Importance-based Sampling (FedAIS) approach. It achieves substantial computational cost saving by focusing the limited resources on training important nodes, while reducing communication overhead via adaptive historical embedding synchronization. The proposed adaptive importance-based sampling method jointly considers the graph structural heterogeneity and the optimization dynamics to achieve optimal trade-off between efficiency and accuracy. Extensive evaluations against five state-of-the-art baselines on five real-world graph datasets show that FedAIS achieves comparable or up to 3.23% higher test accuracy, while saving communication and computation costs by 91.77% and 85.59%.
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%.
Graph signal processing deals with algorithms and signal representations that leverage graph structures for multivariate data analysis. Often said graph topology is not readily available and may be time-varying, hence (dynamic) graph structure learning from nodal (e.g., sensor) observations becomes a critical first step. In this paper, we develop a novel algorithm for online graph learning using observation streams, assumed to be smooth on the latent graph. Unlike batch algorithms for topology identification from smooth signals, our modus operandi is to process graph signals sequentially and thus keep memory and computational costs in check. To solve the resulting smoothness-regularized, time-varying inverse problem, we develop online and lightweight iterations built upon the proximal variant of the alternating direction method of multipliers (ADMM), well known for its fast convergence in batch settings. The proximal term in the topology updates seamlessly implements a temporal-variation regularization, and we argue the online procedure exhibits sublinear static regret under some simplifying assumptions. Reproducible experiments with synthetic and real graphs demonstrate the effectiveness of our method in adapting to streaming signals and tracking slowly-varying network connectivity. The proposed approach also exhibits better tracking performance (in terms of suboptimality), when compared to state-of-the-art online graph learning baselines.
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.