The identification of important nodes with strong propagation capabilities in road networks is a vital topic in urban planning. Existing methods for evaluating the importance of nodes in traffic networks only consider topological information and traffic volumes, the diversity of the traffic characteristics in road networks, such as the number of lanes and average speed of road segments, is ignored, thus limiting their performance. To solve this problem, we propose a graph learning-based framework (MGL2Rank) that integrates the rich characteristics of road networks to rank the importance of nodes. This framework comprises an embedding module containing a sampling algorithm (MGWalk) and an encoder network to learn the latent representations for each road segment. MGWalk utilizes multigraph fusion to capture the topology of road networks and establish associations between road segments based on their attributes. The obtained node representation is then used to learn the importance ranking of the road segments. Finally, a synthetic dataset is constructed for ranking tasks based on the regional road network of Shenyang City, and the ranking results on this dataset demonstrate the effectiveness of our method. The data and source code for MGL2Rank are available at https://github.com/iCityLab/MGL2Rank.
Many real-world graph learning tasks require handling dynamic graphs where new nodes and edges emerge. Dynamic graph learning methods commonly suffer from the catastrophic forgetting problem, where knowledge learned for previous graphs is overwritten by updates for new graphs. To alleviate the problem, continual graph learning methods are proposed. However, existing continual graph learning methods aim to learn new patterns and maintain old ones with the same set of parameters of fixed size, and thus face a fundamental tradeoff between both goals. In this paper, we propose Parameter Isolation GNN (PI-GNN) for continual learning on dynamic graphs that circumvents the tradeoff via parameter isolation and expansion. Our motivation lies in that different parameters contribute to learning different graph patterns. Based on the idea, we expand model parameters to continually learn emerging graph patterns. Meanwhile, to effectively preserve knowledge for unaffected patterns, we find parameters that correspond to them via optimization and freeze them to prevent them from being rewritten. Experiments on eight real-world datasets corroborate the effectiveness of PI-GNN compared to state-of-the-art baselines.
Link prediction, which consists of predicting edges based on graph features, is a fundamental task in many graph applications. As for several related problems, Graph Neural Networks (GNNs), which are based on an attribute-centric message-passing paradigm, have become the predominant framework for link prediction. GNNs have consistently outperformed traditional topology-based heuristics, but what contributes to their performance? Are there simpler approaches that achieve comparable or better results? To answer these questions, we first identify important limitations in how GNN-based link prediction methods handle the intrinsic class imbalance of the problem -- due to the graph sparsity -- in their training and evaluation. Moreover, we propose Gelato, a novel topology-centric framework that applies a topological heuristic to a graph enhanced by attribute information via graph learning. Our model is trained end-to-end with an N-pair loss on an unbiased training set to address class imbalance. Experiments show that Gelato is 145% more accurate, trains 11 times faster, infers 6,000 times faster, and has less than half of the trainable parameters compared to state-of-the-art GNNs for link prediction.
Feature selection (FS) plays an important role in machine learning, which extracts important features and accelerates the learning process. In this paper, we propose a deep FS method that simultaneously conducts feature selection and differentiable $ k $-NN graph learning based on the Dirichlet Energy. The Dirichlet Energy identifies important features by measuring their smoothness on the graph structure, and facilitates the learning of a new graph that reflects the inherent structure in new feature subspace. We employ Optimal Transport theory to address the non-differentiability issue of learning $ k $-NN graphs in neural networks, which theoretically makes our method applicable to other graph neural networks for dynamic graph learning. Furthermore, the proposed framework is interpretable, since all modules are designed algorithmically. We validate the effectiveness of our model with extensive experiments on both synthetic and real-world datasets.
Graph convolutional networks (GCN) are viewed as one of the most popular representations among the variants of graph neural networks over graph data and have shown powerful performance in empirical experiments. That $\ell_2$-based graph smoothing enforces the global smoothness of GCN, while (soft) $\ell_1$-based sparse graph learning tends to promote signal sparsity to trade for discontinuity. This paper aims to quantify the trade-off of GCN between smoothness and sparsity, with the help of a general $\ell_p$-regularized $(1<p\leq 2)$ stochastic learning proposed within. While stability-based generalization analyses have been given in prior work for a second derivative objectiveness function, our $\ell_p$-regularized learning scheme does not satisfy such a smooth condition. To tackle this issue, we propose a novel SGD proximal algorithm for GCNs with an inexact operator. For a single-layer GCN, we establish an explicit theoretical understanding of GCN with the $\ell_p$-regularized stochastic learning by analyzing the stability of our SGD proximal algorithm. We conduct multiple empirical experiments to validate our theoretical findings.
This paper presents a novel transformer architecture for graph representation learning. The core insight of our method is to fully consider the information propagation among nodes and edges in a graph when building the attention module in the transformer blocks. Specifically, we propose a new attention mechanism called Graph Propagation Attention (GPA). It explicitly passes the information among nodes and edges in three ways, i.e. node-to-node, node-to-edge, and edge-to-node, which is essential for learning graph-structured data. On this basis, we design an effective transformer architecture named Graph Propagation Transformer (GPTrans) to further help learn graph data. We verify the performance of GPTrans in a wide range of graph learning experiments on several benchmark datasets. These results show that our method outperforms many state-of-the-art transformer-based graph models with better performance. The code will be released at https://github.com/czczup/GPTrans.
Learning on graphs is becoming prevalent in a wide range of applications including social networks, robotics, communication, medicine, etc. These datasets belonging to entities often contain critical private information. The utilization of data for graph learning applications is hampered by the growing privacy concerns from users on data sharing. Existing privacy-preserving methods pre-process the data to extract user-side features, and only these features are used for subsequent learning. Unfortunately, these methods are vulnerable to adversarial attacks to infer private attributes. We present a novel privacy-respecting framework for distributed graph learning and graph-based machine learning. In order to perform graph learning and other downstream tasks on the server side, this framework aims to learn features as well as distances without requiring actual features while preserving the original structural properties of the raw data. The proposed framework is quite generic and highly adaptable. We demonstrate the utility of the Euclidean space, but it can be applied with any existing method of distance approximation and graph learning for the relevant spaces. Through extensive experimentation on both synthetic and real datasets, we demonstrate the efficacy of the framework in terms of comparing the results obtained without data sharing to those obtained with data sharing as a benchmark. This is, to our knowledge, the first privacy-preserving distributed graph learning framework.
Deep graph clustering has recently received significant attention due to its ability to enhance the representation learning capabilities of models in unsupervised scenarios. Nevertheless, deep clustering for temporal graphs, which could capture crucial dynamic interaction information, has not been fully explored. It means that in many clustering-oriented real-world scenarios, temporal graphs can only be processed as static graphs. This not only causes the loss of dynamic information but also triggers huge computational consumption. To solve the problem, we propose a general framework for deep Temporal Graph Clustering called TGC, which introduces deep clustering techniques to suit the interaction sequence-based batch-processing pattern of temporal graphs. In addition, we discuss differences between temporal graph clustering and static graph clustering from several levels. To verify the superiority of the proposed framework TGC, we conduct extensive experiments. The experimental results show that temporal graph clustering enables more flexibility in finding a balance between time and space requirements, and our framework can effectively improve the performance of existing temporal graph learning methods. The code is released: https://github.com/MGitHubL/Deep-Temporal-Graph-Clustering.
The task of root cause analysis (RCA) is to identify the root causes of system faults/failures by analyzing system monitoring data. Efficient RCA can greatly accelerate system failure recovery and mitigate system damages or financial losses. However, previous research has mostly focused on developing offline RCA algorithms, which often require manually initiating the RCA process, a significant amount of time and data to train a robust model, and then being retrained from scratch for a new system fault. In this paper, we propose CORAL, a novel online RCA framework that can automatically trigger the RCA process and incrementally update the RCA model. CORAL consists of Trigger Point Detection, Incremental Disentangled Causal Graph Learning, and Network Propagation-based Root Cause Localization. The Trigger Point Detection component aims to detect system state transitions automatically and in near-real-time. To achieve this, we develop an online trigger point detection approach based on multivariate singular spectrum analysis and cumulative sum statistics. To efficiently update the RCA model, we propose an incremental disentangled causal graph learning approach to decouple the state-invariant and state-dependent information. After that, CORAL applies a random walk with restarts to the updated causal graph to accurately identify root causes. The online RCA process terminates when the causal graph and the generated root cause list converge. Extensive experiments on three real-world datasets with case studies demonstrate the effectiveness and superiority of the proposed framework.
Graph neural networks (GNNs) realize great success in graph learning but suffer from performance loss when meeting heterophily, i.e. neighboring nodes are dissimilar, due to their local and uniform aggregation. Existing attempts of heterophilous GNNs incorporate long-range or global aggregations to distinguish nodes in the graph. However, these aggregations usually require iteratively maintaining and updating full-graph information, which limits their efficiency when applying to large-scale graphs. In this paper, we propose SIGMA, an efficient global heterophilous GNN aggregation integrating the structural similarity measurement SimRank. Our theoretical analysis illustrates that SIGMA inherently captures distant global similarity even under heterophily, that conventional approaches can only achieve after iterative aggregations. Furthermore, it enjoys efficient one-time computation with a complexity only linear to the node set size $\mathcal{O}(n)$. Comprehensive evaluation demonstrates that SIGMA achieves state-of-the-art performance with superior aggregation and overall efficiency. Notably, it obtains $5\times$ acceleration on the large-scale heterophily dataset pokec with over 30 million edges compared to the best baseline aggregation.
Heterogeneous graph neural networks (HGNNs) can learn from typed and relational graph data more effectively than conventional GNNs. With larger parameter spaces, HGNNs may require more training data, which is often scarce in real-world applications due to privacy regulations (e.g., GDPR). Federated graph learning (FGL) enables multiple clients to train a GNN collaboratively without sharing their local data. However, existing FGL methods mainly focus on homogeneous GNNs or knowledge graph embeddings; few have considered heterogeneous graphs and HGNNs. In federated heterogeneous graph learning, clients may have private graph schemas. Conventional FL/FGL methods attempting to define a global HGNN model would violate schema privacy. To address these challenges, we propose FedHGN, a novel and general FGL framework for HGNNs. FedHGN adopts schema-weight decoupling to enable schema-agnostic knowledge sharing and employs coefficients alignment to stabilize the training process and improve HGNN performance. With better privacy preservation, FedHGN consistently outperforms local training and conventional FL methods on three widely adopted heterogeneous graph datasets with varying client numbers. The code is available at https://github.com/cynricfu/FedHGN .
Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance degradation under complex real-world scenarios due to various factors, e.g., label scarcity and domain shift. In this paper, we propose a self-ensembling multigraph neural network (SemiGNN-PPI) that can effectively predict PPIs while being both efficient and generalizable. In SemiGNN-PPI, we not only model the protein correlations but explore the label dependencies by constructing and processing multiple graphs from the perspectives of both features and labels in the graph learning process. We further marry GNN with Mean Teacher to effectively leverage unlabeled graph-structured PPI data for self-ensemble graph learning. We also design multiple graph consistency constraints to align the student and teacher graphs in the feature embedding space, enabling the student model to better learn from the teacher model by incorporating more relationships. Extensive experiments on PPI datasets of different scales with different evaluation settings demonstrate that SemiGNN-PPI outperforms state-of-the-art PPI prediction methods, particularly in challenging scenarios such as training with limited annotations and testing on unseen data.
Attention-based graph neural networks (GNNs), such as graph attention networks (GATs), have become popular neural architectures for processing graph-structured data and learning node embeddings. Despite their empirical success, these models rely on labeled data and the theoretical properties of these models have yet to be fully understood. In this work, we propose a novel attention-based node embedding framework for graphs. Our framework builds upon a hierarchical kernel for multisets of subgraphs around nodes (e.g. neighborhoods) and each kernel leverages the geometry of a smooth statistical manifold to compare pairs of multisets, by "projecting" the multisets onto the manifold. By explicitly computing node embeddings with a manifold of Gaussian mixtures, our method leads to a new attention mechanism for neighborhood aggregation. We provide theoretical insights into generalizability and expressivity of our embeddings, contributing to a deeper understanding of attention-based GNNs. We propose both efficient unsupervised and supervised methods for learning the embeddings. Through experiments on several node classification benchmarks, we demonstrate that our proposed method outperforms existing attention-based graph models like GATs. Our code is available at https://github.com/BorgwardtLab/fisher_information_embedding.
The bipartite graph structure has shown its promising ability in facilitating the subspace clustering and spectral clustering algorithms for large-scale datasets. To avoid the post-processing via k-means during the bipartite graph partitioning, the constrained Laplacian rank (CLR) is often utilized for constraining the number of connected components (i.e., clusters) in the bipartite graph, which, however, neglects the distribution (or normalization) of these connected components and may lead to imbalanced or even ill clusters. Despite the significant success of normalized cut (Ncut) in general graphs, it remains surprisingly an open problem how to enforce a one-step normalized cut for bipartite graphs, especially with linear-time complexity. In this paper, we first characterize a novel one-step bipartite graph cut (OBCut) criterion with normalized constraints, and theoretically prove its equivalence to a trace maximization problem. Then we extend this cut criterion to a scalable subspace clustering approach, where adaptive anchor learning, bipartite graph learning, and one-step normalized bipartite graph partitioning are simultaneously modeled in a unified objective function, and an alternating optimization algorithm is further designed to solve it in linear time. Experiments on a variety of general and large-scale datasets demonstrate the effectiveness and scalability of our approach.
Federated recommendation systems employ federated learning techniques to safeguard user privacy by transmitting model parameters instead of raw user data between user devices and the central server. Nevertheless, the current federated recommender system faces challenges such as heterogeneity and personalization, model performance degradation, and communication bottleneck. Previous studies have attempted to address these issues, but none have been able to solve them simultaneously. In this paper, we propose a novel framework, named PerFedRec++, to enhance the personalized federated recommendation with self-supervised pre-training. Specifically, we utilize the privacy-preserving mechanism of federated recommender systems to generate two augmented graph views, which are used as contrastive tasks in self-supervised graph learning to pre-train the model. Pre-training enhances the performance of federated models by improving the uniformity of representation learning. Also, by providing a better initial state for federated training, pre-training makes the overall training converge faster, thus alleviating the heavy communication burden. We then construct a collaborative graph to learn the client representation through a federated graph neural network. Based on these learned representations, we cluster users into different user groups and learn personalized models for each cluster. Each user learns a personalized model by combining the global federated model, the cluster-level federated model, and its own fine-tuned local model. Experiments on three real-world datasets show that our proposed method achieves superior performance over existing methods.
Proposing an effective and flexible matrix to represent a graph is a fundamental challenge that has been explored from multiple perspectives, e.g., filtering in Graph Fourier Transforms. In this work, we develop a novel and general framework which unifies many existing GNN models from the view of parameterized decomposition and filtering, and show how it helps to enhance the flexibility of GNNs while alleviating the smoothness and amplification issues of existing models. Essentially, we show that the extensively studied spectral graph convolutions with learnable polynomial filters are constrained variants of this formulation, and releasing these constraints enables our model to express the desired decomposition and filtering simultaneously. Based on this generalized framework, we develop models that are simple in implementation but achieve significant improvements and computational efficiency on a variety of graph learning tasks. Code is available at https://github.com/qslim/PDF.
To characterize atypical brain dynamics under diseases, prevalent studies investigate functional magnetic resonance imaging (fMRI). However, most of the existing analyses compress rich spatial-temporal information as the brain functional networks (BFNs) and directly investigate the whole-brain network without neurological priors about functional subnetworks. We thus propose a novel graph learning framework to mine fMRI signals with topological priors from brain parcellation for disease diagnosis. Specifically, we 1) detect diagnosis-related temporal features using a "Transformer" for a higher-level BFN construction, and process it with a following graph convolutional network, and 2) apply an attention-based multiple instance learning strategy to emphasize the disease-affected subnetworks to further enhance the diagnosis performance and interpretability. Experiments demonstrate higher effectiveness of our method than compared methods in the diagnosis of early mild cognitive impairment. More importantly, our method is capable of localizing crucial brain subnetworks during the diagnosis, providing insights into the pathogenic source of mild cognitive impairment.
Laplacian regularized stratified models (LRSM) are models that utilize the explicit or implicit network structure of the sub-problems as defined by the categorical features called strata (e.g., age, region, time, forecast horizon, etc.), and draw upon data from neighboring strata to enhance the parameter learning of each sub-problem. They have been widely applied in machine learning and signal processing problems, including but not limited to time series forecasting, representation learning, graph clustering, max-margin classification, and general few-shot learning. Nevertheless, existing works on LRSM have either assumed a known graph or are restricted to specific applications. In this paper, we start by showing the importance and sensitivity of graph weights in LRSM, and provably show that the sensitivity can be arbitrarily large when the parameter scales and sample sizes are heavily imbalanced across nodes. We then propose a generic approach to jointly learn the graph while fitting the model parameters by solving a single optimization problem. We interpret the proposed formulation from both a graph connectivity viewpoint and an end-to-end Bayesian perspective, and propose an efficient algorithm to solve the problem. Convergence guarantees of the proposed optimization algorithm is also provided despite the lack of global strongly smoothness of the Laplacian regularization term typically required in the existing literature, which may be of independent interest. Finally, we illustrate the efficiency of our approach compared to existing methods by various real-world numerical examples.
Graph Transformer is gaining increasing attention in the field of machine learning and has demonstrated state-of-the-art performance on benchmarks for graph representation learning. However, as current implementations of Graph Transformer primarily focus on learning representations of small-scale graphs, the quadratic complexity of the global self-attention mechanism presents a challenge for full-batch training when applied to larger graphs. Additionally, conventional sampling-based methods fail to capture necessary high-level contextual information, resulting in a significant loss of performance. In this paper, we introduce the Hierarchical Scalable Graph Transformer (HSGT) as a solution to these challenges. HSGT successfully scales the Transformer architecture to node representation learning tasks on large-scale graphs, while maintaining high performance. By utilizing graph hierarchies constructed through coarsening techniques, HSGT efficiently updates and stores multi-scale information in node embeddings at different levels. Together with sampling-based training methods, HSGT effectively captures and aggregates multi-level information on the hierarchical graph using only Transformer blocks. Empirical evaluations demonstrate that HSGT achieves state-of-the-art performance on large-scale benchmarks with graphs containing millions of nodes with high efficiency.
The potential impact of a paper is often quantified by how many citations it will receive. However, most commonly used models may underestimate the influence of newly published papers over time, and fail to encapsulate this dynamics of citation network into the graph. In this study, we construct hierarchical and heterogeneous graphs for target papers with an annual perspective. The constructed graphs can record the annual dynamics of target papers' scientific context information. Then, a novel graph neural network, Hierarchical and Heterogeneous Contrastive Graph Learning Model (H2CGL), is proposed to incorporate heterogeneity and dynamics of the citation network. H2CGL separately aggregates the heterogeneous information for each year and prioritizes the highly-cited papers and relationships among references, citations, and the target paper. It then employs a weighted GIN to capture dynamics between heterogeneous subgraphs over years. Moreover, it leverages contrastive learning to make the graph representations more sensitive to potential citations. Particularly, co-cited or co-citing papers of the target paper with large citation gap are taken as hard negative samples, while randomly dropping low-cited papers could generate positive samples. Extensive experimental results on two scholarly datasets demonstrate that the proposed H2CGL significantly outperforms a series of baseline approaches for both previously and freshly published papers. Additional analyses highlight the significance of the proposed modules. Our codes and settings have been released on Github (https://github.com/ECNU-Text-Computing/H2CGL)