Federated Graph Learning (FGL) has garnered widespread attention by enabling collaborative training on multiple clients for semi-supervised classification tasks. However, most existing FGL studies do not well consider the missing inter-client topology information in real-world scenarios, causing insufficient feature aggregation of multi-hop neighbor clients during model training. Moreover, the classic FGL commonly adopts the FedAvg but neglects the high training costs when the number of clients expands, resulting in the overload of a single edge server. To address these important challenges, we propose a novel FGL framework, named SpreadFGL, to promote the information flow in edge-client collaboration and extract more generalized potential relationships between clients. In SpreadFGL, an adaptive graph imputation generator incorporated with a versatile assessor is first designed to exploit the potential links between subgraphs, without sharing raw data. Next, a new negative sampling mechanism is developed to make SpreadFGL concentrate on more refined information in downstream tasks. To facilitate load balancing at the edge layer, SpreadFGL follows a distributed training manner that enables fast model convergence. Using real-world testbed and benchmark graph datasets, extensive experiments demonstrate the effectiveness of the proposed SpreadFGL. The results show that SpreadFGL achieves higher accuracy and faster convergence against state-of-the-art algorithms.
Homophily principle, \ie{} nodes with the same labels or similar attributes are more likely to be connected, has been commonly believed to be the main reason for the superiority of Graph Neural Networks (GNNs) over traditional Neural Networks (NNs) on graph-structured data, especially on node-level tasks. However, recent work has identified a non-trivial set of datasets where GNN's performance compared to the NN's is not satisfactory. Heterophily, i.e. low homophily, has been considered the main cause of this empirical observation. People have begun to revisit and re-evaluate most existing graph models, including graph transformer and its variants, in the heterophily scenario across various kinds of graphs, e.g. heterogeneous graphs, temporal graphs and hypergraphs. Moreover, numerous graph-related applications are found to be closely related to the heterophily problem. In the past few years, considerable effort has been devoted to studying and addressing the heterophily issue. In this survey, we provide a comprehensive review of the latest progress on heterophilic graph learning, including an extensive summary of benchmark datasets and evaluation of homophily metrics on synthetic graphs, meticulous classification of the most updated supervised and unsupervised learning methods, thorough digestion of the theoretical analysis on homophily/heterophily, and broad exploration of the heterophily-related applications. Notably, through detailed experiments, we are the first to categorize benchmark heterophilic datasets into three sub-categories: malignant, benign and ambiguous heterophily. Malignant and ambiguous datasets are identified as the real challenging datasets to test the effectiveness of new models on the heterophily challenge. Finally, we propose several challenges and future directions for heterophilic graph representation learning.
Mini-batch Graph Transformer (MGT), as an emerging graph learning model, has demonstrated significant advantages in semi-supervised node prediction tasks with improved computational efficiency and enhanced model robustness. However, existing methods for processing local information either rely on sampling or simple aggregation, which respectively result in the loss and squashing of critical neighbor information.Moreover, the limited number of nodes in each mini-batch restricts the model's capacity to capture the global characteristic of the graph. In this paper, we propose LGMformer, a novel MGT model that employs a two-stage augmented interaction strategy, transitioning from local to global perspectives, to address the aforementioned bottlenecks.The local interaction augmentation (LIA) presents a neighbor-target interaction Transformer (NTIformer) to acquire an insightful understanding of the co-interaction patterns between neighbors and the target node, resulting in a locally effective token list that serves as input for the MGT. In contrast, global interaction augmentation (GIA) adopts a cross-attention mechanism to incorporate entire graph prototypes into the target node epresentation, thereby compensating for the global graph information to ensure a more comprehensive perception. To this end, LGMformer achieves the enhancement of node representations under the MGT paradigm.Experimental results related to node classification on the ten benchmark datasets demonstrate the effectiveness of the proposed method. Our code is available at https://github.com/l-wd/LGMformer.
Mixup has shown considerable success in mitigating the challenges posed by limited labeled data in image classification. By synthesizing samples through the interpolation of features and labels, Mixup effectively addresses the issue of data scarcity. However, it has rarely been explored in graph learning tasks due to the irregularity and connectivity of graph data. Specifically, in node classification tasks, Mixup presents a challenge in creating connections for synthetic data. In this paper, we propose Geometric Mixup (GeoMix), a simple and interpretable Mixup approach leveraging in-place graph editing. It effectively utilizes geometry information to interpolate features and labels with those from the nearby neighborhood, generating synthetic nodes and establishing connections for them. We conduct theoretical analysis to elucidate the rationale behind employing geometry information for node Mixup, emphasizing the significance of locality enhancement-a critical aspect of our method's design. Extensive experiments demonstrate that our lightweight Geometric Mixup achieves state-of-the-art results on a wide variety of standard datasets with limited labeled data. Furthermore, it significantly improves the generalization capability of underlying GNNs across various challenging out-of-distribution generalization tasks. Our code is available at https://github.com/WtaoZhao/geomix.
Graph transformers are a recent advancement in machine learning, offering a new class of neural network models for graph-structured data. The synergy between transformers and graph learning demonstrates strong performance and versatility across various graph-related tasks. This survey provides an in-depth review of recent progress and challenges in graph transformer research. We begin with foundational concepts of graphs and transformers. We then explore design perspectives of graph transformers, focusing on how they integrate graph inductive biases and graph attention mechanisms into the transformer architecture. Furthermore, we propose a taxonomy classifying graph transformers based on depth, scalability, and pre-training strategies, summarizing key principles for effective development of graph transformer models. Beyond technical analysis, we discuss the applications of graph transformer models for node-level, edge-level, and graph-level tasks, exploring their potential in other application scenarios as well. Finally, we identify remaining challenges in the field, such as scalability and efficiency, generalization and robustness, interpretability and explainability, dynamic and complex graphs, as well as data quality and diversity, charting future directions for graph transformer research.
Graph mining has become crucial in fields such as social science, finance, and cybersecurity. Many large-scale real-world networks exhibit both heterogeneity, where multiple node and edge types exist in the graph, and heterophily, where connected nodes may have dissimilar labels and attributes. However, existing benchmarks primarily focus on either heterophilic homogeneous graphs or homophilic heterogeneous graphs, leaving a significant gap in understanding how models perform on graphs with both heterogeneity and heterophily. To bridge this gap, we introduce H2GB, a large-scale node-classification graph benchmark that brings together the complexities of both the heterophily and heterogeneity properties of real-world graphs. H2GB encompasses 9 real-world datasets spanning 5 diverse domains, 28 baseline models, and a unified benchmarking library with a standardized data loader, evaluator, unified modeling framework, and an extensible framework for reproducibility. We establish a standardized workflow supporting both model selection and development, enabling researchers to easily benchmark graph learning methods. Extensive experiments across 28 baselines reveal that current methods struggle with heterophilic and heterogeneous graphs, underscoring the need for improved approaches. Finally, we present a new variant of the model, H2G-former, developed following our standardized workflow, that excels at this challenging benchmark. Both the benchmark and the framework are publicly available at Github and PyPI, with documentation hosted at https://junhongmit.github.io/H2GB.
Existing WSI analysis methods lie on the consensus that histopathological characteristics of tumors are significant guidance for cancer diagnostics. Particularly, as the evolution of cancers is a continuous process, the correlations and differences across various stages, anatomical locations and patients should be taken into account. However, recent research mainly focuses on the inner-contextual information in a single WSI, ignoring the correlations between slides. To verify whether introducing the slide inter-correlations can bring improvements to WSI representation learning, we propose a generic WSI analysis pipeline SlideGCD that considers the existing multi-instance learning (MIL) methods as the backbone and forge the WSI classification task as a node classification problem. More specifically, SlideGCD declares a node buffer that stores previous slide embeddings for subsequent extensive slide-based graph construction and conducts graph learning to explore the inter-correlations implied in the slide-based graph. Moreover, we frame the MIL classifier and graph learning into two parallel workflows and deploy the knowledge distillation to transfer the differentiable information to the graph neural network. The consistent performance boosting, brought by SlideGCD, of four previous state-of-the-art MIL methods is observed on two TCGA benchmark datasets. The code is available at https://github.com/HFUT-miaLab/SlideGCD.
In recent years, Multi-View Clustering (MVC) has attracted increasing attention for its potential to reduce the annotation burden associated with large datasets. The aim of MVC is to exploit the inherent consistency and complementarity among different views, thereby integrating information from multiple perspectives to improve clustering outcomes. Despite extensive research in MVC, most existing methods focus predominantly on harnessing complementary information across views to enhance clustering effectiveness, often neglecting the structural information among samples, which is crucial for exploring sample correlations. To address this gap, we introduce a novel framework, termed Structured Latent Representation Learning based Multi-View Clustering method (SLRL). SLRL leverages both the complementary and structural information. Initially, it learns a common latent representation for all views. Subsequently, to exploit the structural information among samples, a k-nearest neighbor graph is constructed from this common latent representation. This graph facilitates enhanced sample interaction through graph learning techniques, leading to a structured latent representation optimized for clustering. Extensive experiments demonstrate that SLRL not only competes well with existing methods but also sets new benchmarks in various multi-view datasets.
Continuous-Time Dynamic Graph (CTDG) precisely models evolving real-world relationships, drawing heightened interest in dynamic graph learning across academia and industry. However, existing CTDG models encounter challenges stemming from noise and limited historical data. Graph Data Augmentation (GDA) emerges as a critical solution, yet current approaches primarily focus on static graphs and struggle to effectively address the dynamics inherent in CTDGs. Moreover, these methods often demand substantial domain expertise for parameter tuning and lack theoretical guarantees for augmentation efficacy. To address these issues, we propose Conda, a novel latent diffusion-based GDA method tailored for CTDGs. Conda features a sandwich-like architecture, incorporating a Variational Auto-Encoder (VAE) and a conditional diffusion model, aimed at generating enhanced historical neighbor embeddings for target nodes. Unlike conventional diffusion models trained on entire graphs via pre-training, Conda requires historical neighbor sequence embeddings of target nodes for training, thus facilitating more targeted augmentation. We integrate Conda into the CTDG model and adopt an alternating training strategy to optimize performance. Extensive experimentation across six widely used real-world datasets showcases the consistent performance improvement of our approach, particularly in scenarios with limited historical data.
Tripartite graph-based recommender systems markedly diverge from traditional models by recommending unique combinations such as user groups and item bundles. Despite their effectiveness, these systems exacerbate the longstanding cold-start problem in traditional recommender systems, because any number of user groups or item bundles can be formed among users or items. To address this issue, we introduce a Consistency and Discrepancy-based graph contrastive learning method for tripartite graph-based Recommendation. This approach leverages two novel meta-path-based metrics consistency and discrepancy to capture nuanced, implicit associations between the recommended objects and the recommendees. These metrics, indicative of high-order similarities, can be efficiently calculated with infinite graph convolutional networks layers under a multi-objective optimization framework, using the limit theory of GCN.
Graph classification benchmarks, vital for assessing and developing graph neural networks (GNNs), have recently been scrutinized, as simple methods like MLPs have demonstrated comparable performance. This leads to an important question: Do these benchmarks effectively distinguish the advancements of GNNs over other methodologies? If so, how do we quantitatively measure this effectiveness? In response, we first propose an empirical protocol based on a fair benchmarking framework to investigate the performance discrepancy between simple methods and GNNs. We further propose a novel metric to quantify the dataset effectiveness by considering both dataset complexity and model performance. To the best of our knowledge, our work is the first to thoroughly study and provide an explicit definition for dataset effectiveness in the graph learning area. Through testing across 16 real-world datasets, we found our metric to align with existing studies and intuitive assumptions. Finally, we explore the causes behind the low effectiveness of certain datasets by investigating the correlation between intrinsic graph properties and class labels, and we developed a novel technique supporting the correlation-controllable synthetic dataset generation. Our findings shed light on the current understanding of benchmark datasets, and our new platform could fuel the future evolution of graph classification benchmarks.
Recent advances in learning multi-modal representation have witnessed the success in biomedical domains. While established techniques enable handling multi-modal information, the challenges are posed when extended to various clinical modalities and practical modalitymissing setting due to the inherent modality gaps. To tackle these, we propose an innovative Modality-prompted Heterogeneous Graph for Omnimodal Learning (GTP-4o), which embeds the numerous disparate clinical modalities into a unified representation, completes the deficient embedding of missing modality and reformulates the cross-modal learning with a graph-based aggregation. Specially, we establish a heterogeneous graph embedding to explicitly capture the diverse semantic properties on both the modality-specific features (nodes) and the cross-modal relations (edges). Then, we design a modality-prompted completion that enables completing the inadequate graph representation of missing modality through a graph prompting mechanism, which generates hallucination graphic topologies to steer the missing embedding towards the intact representation. Through the completed graph, we meticulously develop a knowledge-guided hierarchical cross-modal aggregation consisting of a global meta-path neighbouring to uncover the potential heterogeneous neighbors along the pathways driven by domain knowledge, and a local multi-relation aggregation module for the comprehensive cross-modal interaction across various heterogeneous relations. We assess the efficacy of our methodology on rigorous benchmarking experiments against prior state-of-the-arts. In a nutshell, GTP-4o presents an initial foray into the intriguing realm of embedding, relating and perceiving the heterogeneous patterns from various clinical modalities holistically via a graph theory. Project page: https://gtp-4-o.github.io/.
We present the MEEG dataset, a multi-modal collection of music-induced electroencephalogram (EEG) recordings designed to capture emotional responses to various musical stimuli across different valence and arousal levels. This public dataset facilitates an in-depth examination of brainwave patterns within musical contexts, providing a robust foundation for studying brain network topology during emotional processing. Leveraging the MEEG dataset, we introduce the Attention-based Temporal Learner with Dynamic Graph Neural Network (AT-DGNN), a novel framework for EEG-based emotion recognition. This model combines an attention mechanism with a dynamic graph neural network (DGNN) to capture intricate EEG dynamics. The AT-DGNN achieves state-of-the-art (SOTA) performance with an accuracy of 83.74% in arousal recognition and 86.01% in valence recognition, outperforming existing SOTA methods. Comparative analysis with traditional datasets, such as DEAP, further validates the model's effectiveness and underscores the potency of music as an emotional stimulus. This study advances graph-based learning methodology in brain-computer interfaces (BCI), significantly improving the accuracy of EEG-based emotion recognition. The MEEG dataset and source code are publicly available at https://github.com/xmh1011/AT-DGNN.
Peptides are essential in biological processes and therapeutics. In this study, we introduce Multi-Peptide, an innovative approach that combines transformer-based language models with Graph Neural Networks (GNNs) to predict peptide properties. We combine PeptideBERT, a transformer model tailored for peptide property prediction, with a GNN encoder to capture both sequence-based and structural features. By employing Contrastive Language-Image Pre-training (CLIP), Multi-Peptide aligns embeddings from both modalities into a shared latent space, thereby enhancing the model's predictive accuracy. Evaluations on hemolysis and nonfouling datasets demonstrate Multi-Peptide's robustness, achieving state-of-the-art 86.185% accuracy in hemolysis prediction. This study highlights the potential of multimodal learning in bioinformatics, paving the way for accurate and reliable predictions in peptide-based research and applications.
This work addresses multistationarity of fully open reaction networks equipped with mass action kinetics. We improve upon the existing results relating existence of positive feedback loops in a reaction network and multistationarity; and we provide a novel deterministic operation to generate new non-multistationary networks. This is interesting because while there were many operations to create infinitely many new multistationary networks from a multistationary example, this is the first such operation for the non-multistationary counterpart. Such tools for the generation of example networks have a use-case in the application of data science to reaction network theory. We demonstrate this by using the new data, along with a novel graph representation of reaction networks that is unique up to a permutation on the name of species of the network, to train a graph attention neural network model to predict multistationarity of reaction networks. This is the first time machine learning tools being used for studying classification problems of reaction networks.
Generic deep learning (DL) networks for image restoration like denoising and interpolation lack mathematical interpretability, require voluminous training data to tune a large parameter set, and are fragile in the face of covariate shift. To address these shortcomings, we build interpretable networks by unrolling variants of a graph-based optimization algorithm of different complexities. Specifically, for a general linear image formation model, we first formulate a convex quadratic programming (QP) problem with a new $\ell_2$-norm graph smoothness prior called gradient graph Laplacian regularizer (GGLR) that promotes piecewise planar (PWP) signal reconstruction. To solve the posed unconstrained QP problem, instead of computing a linear system solution straightforwardly, we introduce a variable number of auxiliary variables and correspondingly design a family of ADMM algorithms. We then unroll them into variable-complexity feed-forward networks, amenable to parameter tuning via back-propagation. More complex unrolled networks require more labeled data to train more parameters, but have better overall performance. The unrolled networks have periodic insertions of a graph learning module, akin to a self-attention mechanism in a transformer architecture, to learn pairwise similarity structure inherent in data. Experimental results show that our unrolled networks perform competitively to generic DL networks in image restoration quality while using only a fraction of parameters, and demonstrate improved robustness to covariate shift.
Recent advancements in graph learning have revolutionized the way to understand and analyze data with complex structures. Notably, Graph Neural Networks (GNNs), i.e. neural network architectures designed for learning graph representations, have become a popular paradigm. With these models being usually characterized by intuition-driven design or highly intricate components, placing them within the theoretical analysis framework to distill the core concepts, helps understand the key principles that drive the functionality better and guide further development. Given this surge in interest, this article provides a comprehensive summary of the theoretical foundations and breakthroughs concerning the approximation and learning behaviors intrinsic to prevalent graph learning models. Encompassing discussions on fundamental aspects such as expressiveness power, generalization, optimization, and unique phenomena such as over-smoothing and over-squashing, this piece delves into the theoretical foundations and frontier driving the evolution of graph learning. In addition, this article also presents several challenges and further initiates discussions on possible solutions.
Industrial processes generate vast amounts of time series data, yet extracting meaningful relationships and insights remains challenging. This paper introduces a framework for automated knowledge graph learning from time series data, specifically tailored for industrial applications. Our framework addresses the complexities inherent in industrial datasets, transforming them into knowledge graphs that improve decision-making, process optimization, and knowledge discovery. Additionally, it employs Granger causality to identify key attributes that can inform the design of predictive models. To illustrate the practical utility of our approach, we also present a motivating use case demonstrating the benefits of our framework in a real-world industrial scenario. Further, we demonstrate how the automated conversion of time series data into knowledge graphs can identify causal influences or dependencies between important process parameters.
n the area of clustering, multi-view clustering has drawn a lot of research attention by making full use of information from different views. In many practical applications, collecting complete multi-view data without missing views is sometimes expensive and impossible. Therefore, the study in incomplete multi-view clustering has become a trend in the field of clustering analysis. Graph learning-based approach is one of the most effective tools. The essence of graph learning is how to construct the affinity graph or similarity matrix, whose elements depict the similarity of the corresponding sample pairs. In this paper, we propose a new method, called Neighbor Group Structure Preserving-based Consensus Graph Learning (NGSP_CGL), to learn a high-quality consensus graph for incomplete multi-view clustering. Different from the existing graph learning-based works which only focus on the relationship between isolated sample pairs, NGSP_CGL seeks to explore the neighbor group structure corresponding to the nearest neighbor sets of sample pairs and designs a novel but simple nearest neighbor group structure embedding constraint so as to enhance the quality of consensus graph. The experimental results on several datasets demonstrate the effectiveness of NGSP_CGL.
Graph learning models have been widely deployed in collaborative filtering (CF) based recommendation systems. Due to the issue of data sparsity, the graph structure of the original input lacks potential positive preference edges, which significantly reduces the performance of recommendations. In this paper, we study how to enhance the graph structure for CF more effectively, thereby optimizing the representation of graph nodes. Previous works introduced matrix completion techniques into CF, proposing the use of either stochastic completion methods or superficial structure completion to address this issue. However, most of these approaches employ random numerical filling that lack control over noise perturbations and limit the in-depth exploration of higher-order interaction features of nodes, resulting in biased graph representations. In this paper, we propose an Amplify Graph Learning framework based on Sparsity Completion (called AGL-SC). First, we utilize graph neural network to mine direct interaction features between user and item nodes, which are used as the inputs of the encoder. Second, we design a factorization-based method to mine higher-order interaction features. These features serve as perturbation factors in the latent space of the hidden layer to facilitate generative enhancement. Finally, by employing the variational inference, the above multi-order features are integrated to implement the completion and enhancement of missing graph structures. We conducted benchmark and strategy experiments on four real-world datasets related to recommendation tasks. The experimental results demonstrate that AGL-SC significantly outperforms the state-of-the-art methods.