Graph Neural Networks (GNNs) that are based on the message passing (MP) paradigm generally exchange information between 1-hop neighbors to build node representations at each layer. In principle, such networks are not able to capture long-range interactions (LRI) that may be desired or necessary for learning a given task on graphs. Recently, there has been an increasing interest in development of Transformer-based methods for graphs that can consider full node connectivity beyond the original sparse structure, thus enabling the modeling of LRI. However, MP-GNNs that simply rely on 1-hop message passing often fare better in several existing graph benchmarks when combined with positional feature representations, among other innovations, hence limiting the perceived utility and ranking of Transformer-like architectures. Here, we present the Long Range Graph Benchmark (LRGB) with 5 graph learning datasets: PascalVOC-SP, COCO-SP, PCQM-Contact, Peptides-func and Peptides-struct that arguably require LRI reasoning to achieve strong performance in a given task. We benchmark both baseline GNNs and Graph Transformer networks to verify that the models which capture long-range dependencies perform significantly better on these tasks. Therefore, these datasets are suitable for benchmarking and exploration of MP-GNNs and Graph Transformer architectures that are intended to capture LRI.
Attributed graph clustering is one of the most fundamental tasks among graph learning field, the goal of which is to group nodes with similar representations into the same cluster without human annotations. Recent studies based on graph contrastive learning method have achieved remarkable results when exploit graph-structured data. However, most existing methods 1) do not directly address the clustering task, since the representation learning and clustering process are separated; 2) depend too much on data augmentation, which greatly limits the capability of contrastive learning; 3) ignore the contrastive message for clustering tasks, which adversely degenerate the clustering results. In this paper, we propose a Neighborhood Contrast Framework for Attributed Graph Clustering, namely NCAGC, seeking for conquering the aforementioned limitations. Specifically, by leveraging the Neighborhood Contrast Module, the representation of neighbor nodes will be 'push closer' and become clustering-oriented with the neighborhood contrast loss. Moreover, a Contrastive Self-Expression Module is built by minimizing the node representation before and after the self-expression layer to constraint the learning of self-expression matrix. All the modules of NCAGC are optimized in a unified framework, so the learned node representation contains clustering-oriented messages. Extensive experimental results on four attributed graph datasets demonstrate the promising performance of NCAGC compared with 16 state-of-the-art clustering methods. The code is available at https://github.com/wangtong627/NCAGC.
Allowing agents to share information through communication is crucial for solving complex tasks in multi-agent reinforcement learning. In this work, we consider the question of whether a given communication protocol can express an arbitrary policy. By observing that many existing protocols can be viewed as instances of graph neural networks (GNNs), we demonstrate the equivalence of joint action selection to node labelling. With standard GNN approaches provably limited in their expressive capacity, we draw from existing GNN literature and consider augmenting agent observations with: (1) unique agent IDs and (2) random noise. We provide a theoretical analysis as to how these approaches yield universally expressive communication, and also prove them capable of targeting arbitrary sets of actions for identical agents. Empirically, these augmentations are found to improve performance on tasks where expressive communication is required, whilst, in general, the optimal communication protocol is found to be task-dependent.
The graph Transformer emerges as a new architecture and has shown superior performance on various graph mining tasks. In this work, we observe that existing graph Transformers treat nodes as independent tokens and construct a single long sequence composed of all node tokens so as to train the Transformer model, causing it hard to scale to large graphs due to the quadratic complexity on the number of nodes for the self-attention computation. To this end, we propose a Neighborhood Aggregation Graph Transformer (NAGphormer) that treats each node as a sequence containing a series of tokens constructed by our proposed Hop2Token module. For each node, Hop2Token aggregates the neighborhood features from different hops into different representations and thereby produces a sequence of token vectors as one input. In this way, NAGphormer could be trained in a mini-batch manner and thus could scale to large graphs. Moreover, we mathematically show that as compared to a category of advanced Graph Neural Networks (GNNs), the decoupled Graph Convolutional Network, NAGphormer could learn more informative node representations from the multi-hop neighborhoods. Extensive experiments on benchmark datasets from small to large are conducted to demonstrate that NAGphormer consistently outperforms existing graph Transformers and mainstream GNNs. Code is available at https://github.com/JHL-HUST/NAGphormer.
Machine Learning (ML) systems are a building part of the modern tools which impact our daily life in several application domains. Due to their black-box nature, those systems are hardly adopted in application domains (e.g. health, finance) where understanding the decision process is of paramount importance. Explanation methods were developed to explain how the ML model has taken a specific decision for a given case/instance. Graph Counterfactual Explanations (GCE) is one of the explanation techniques adopted in the Graph Learning domain. The existing works of Graph Counterfactual Explanations diverge mostly in the problem definition, application domain, test data, and evaluation metrics, and most existing works do not compare exhaustively against other counterfactual explanation techniques present in the literature. We present GRETEL, a unified framework to develop and test GCE methods in several settings. GRETEL is a highly extensible evaluation framework which promotes the Open Science and the evaluations reproducibility by providing a set of well-defined mechanisms to integrate and manage easily: both real and synthetic datasets, ML models, state-of-the-art explanation techniques, and evaluation measures. To present GRETEL, we show the experiments conducted to integrate and test several synthetic and real datasets with several existing explanation techniques and base ML models.
Frequent and structurally related subgraphs, also known as network motifs, are valuable features of many graph datasets. However, the high computational complexity of identifying motif sets in arbitrary datasets (motif mining) has limited their use in many real-world datasets. By automatically leveraging statistical properties of datasets, machine learning approaches have shown promise in several tasks with combinatorial complexity and are therefore a promising candidate for network motif mining. In this work we seek to facilitate the development of machine learning approaches aimed at motif mining. We propose a formulation of the motif mining problem as a node labelling task. In addition, we build benchmark datasets and evaluation metrics which test the ability of models to capture different aspects of motif discovery such as motif number, size, topology, and scarcity. Next, we propose MotiFiesta, a first attempt at solving this problem in a fully differentiable manner with promising results on challenging baselines. Finally, we demonstrate through MotiFiesta that this learning setting can be applied simultaneously to general-purpose data mining and interpretable feature extraction for graph classification tasks.
Bundle recommendation aims to recommend a bundle of related items to users, which can satisfy the users' various needs with one-stop convenience. Recent methods usually take advantage of both user-bundle and user-item interactions information to obtain informative representations for users and bundles, corresponding to bundle view and item view, respectively. However, they either use a unified view without differentiation or loosely combine the predictions of two separate views, while the crucial cooperative association between the two views' representations is overlooked. In this work, we propose to model the cooperative association between the two different views through cross-view contrastive learning. By encouraging the alignment of the two separately learned views, each view can distill complementary information from the other view, achieving mutual enhancement. Moreover, by enlarging the dispersion of different users/bundles, the self-discrimination of representations is enhanced. Extensive experiments on three public datasets demonstrate that our method outperforms SOTA baselines by a large margin. Meanwhile, our method requires minimal parameters of three set of embeddings (user, bundle, and item) and the computational costs are largely reduced due to more concise graph structure and graph learning module. In addition, various ablation and model studies demystify the working mechanism and justify our hypothesis. Codes and datasets are available at https://github.com/mysbupt/CrossCBR.
Topological deep learning is a rapidly growing field that pertains to the development of deep learning models for data supported on topological domains such as simplicial complexes, cell complexes, and hypergraphs, which generalize many domains encountered in scientific computations. In this paper, we present a unifying deep learning framework built upon a richer data structure that includes widely adopted topological domains. Specifically, we first introduce combinatorial complexes, a novel type of topological domain. Combinatorial complexes can be seen as generalizations of graphs that maintain certain desirable properties. Similar to hypergraphs, combinatorial complexes impose no constraints on the set of relations. In addition, combinatorial complexes permit the construction of hierarchical higher-order relations, analogous to those found in simplicial and cell complexes. Thus, combinatorial complexes generalize and combine useful traits of both hypergraphs and cell complexes, which have emerged as two promising abstractions that facilitate the generalization of graph neural networks to topological spaces. Second, building upon combinatorial complexes and their rich combinatorial and algebraic structure, we develop a general class of message-passing combinatorial complex neural networks (CCNNs), focusing primarily on attention-based CCNNs. We characterize permutation and orientation equivariances of CCNNs, and discuss pooling and unpooling operations within CCNNs in detail. Third, we evaluate the performance of CCNNs on tasks related to mesh shape analysis and graph learning. Our experiments demonstrate that CCNNs have competitive performance as compared to state-of-the-art deep learning models specifically tailored to the same tasks. Our findings demonstrate the advantages of incorporating higher-order relations into deep learning models in different applications.
Graph neural architecture search has sparked much attention as Graph Neural Networks (GNNs) have shown powerful reasoning capability in many relational tasks. However, the currently used graph search space overemphasizes learning node features and neglects mining hierarchical relational information. Moreover, due to diverse mechanisms in the message passing, the graph search space is much larger than that of CNNs. This hinders the straightforward application of classical search strategies for exploring complicated graph search space. We propose Automatic Relation-aware Graph Network Proliferation (ARGNP) for efficiently searching GNNs with a relation-guided message passing mechanism. Specifically, we first devise a novel dual relation-aware graph search space that comprises both node and relation learning operations. These operations can extract hierarchical node/relational information and provide anisotropic guidance for message passing on a graph. Second, analogous to cell proliferation, we design a network proliferation search paradigm to progressively determine the GNN architectures by iteratively performing network division and differentiation. The experiments on six datasets for four graph learning tasks demonstrate that GNNs produced by our method are superior to the current state-of-the-art hand-crafted and search-based GNNs. Codes are available at https://github.com/phython96/ARGNP.
Recent years have witnessed a rapid growth of applying deep spatiotemporal methods in traffic forecasting. However, the prediction of origin-destination (OD) demands is still a challenging problem since the number of OD pairs is usually quadratic to the number of stations. In this case, most of the existing spatiotemporal methods fail to handle spatial relations on such a large scale. To address this problem, this paper provides a dynamic graph representation learning framework for OD demands prediction. In particular, a hierarchical memory updater is first proposed to maintain a time-aware representation for each node, and the representations are updated according to the most recently observed OD trips in continuous-time and multiple discrete-time ways. Second, a spatiotemporal propagation mechanism is provided to aggregate representations of neighbor nodes along a random spatiotemporal route which treats origin and destination as two different semantic entities. Last, an objective function is designed to derive the future OD demands according to the most recent node representations, and also to tackle the data sparsity problem in OD prediction. Extensive experiments have been conducted on two real-world datasets, and the experimental results demonstrate the superiority of the proposed method. The code and data are available at https://github.com/Rising0321/HMOD.
In this paper, we introduce Temporal Multiresolution Graph Neural Networks (TMGNN), the first architecture that both learns to construct the multiscale and multiresolution graph structures and incorporates the time-series signals to capture the temporal changes of the dynamic graphs. We have applied our proposed model to the task of predicting future spreading of epidemic and pandemic based on the historical time-series data collected from the actual COVID-19 pandemic and chickenpox epidemic in several European countries, and have obtained competitive results in comparison to other previous state-of-the-art temporal architectures and graph learning algorithms. We have shown that capturing the multiscale and multiresolution structures of graphs is important to extract either local or global information that play a critical role in understanding the dynamic of a global pandemic such as COVID-19 which started from a local city and spread to the whole world. Our work brings a promising research direction in forecasting and mitigating future epidemics and pandemics.
Graph neural networks (GNNs) continue to achieve state-of-the-art performance on many graph learning tasks, but rely on the assumption that a given graph is a sufficient approximation of the true neighborhood structure. When a system contains higher-order sequential dependencies, we show that the tendency of traditional graph representations to underfit each node's neighborhood causes existing GNNs to generalize poorly. To address this, we propose a novel Deep Graph Ensemble (DGE), which captures neighborhood variance by training an ensemble of GNNs on different neighborhood subspaces of the same node within a higher-order network structure. We show that DGE consistently outperforms existing GNNs on semisupervised and supervised tasks on six real-world data sets with known higher-order dependencies, even under a similar parameter budget. We demonstrate that learning diverse and accurate base classifiers is central to DGE's success, and discuss the implications of these findings for future work on ensembles of GNNs.
Spatio-temporal graph learning is a key method for urban computing tasks, such as traffic flow, taxi demand and air quality forecasting. Due to the high cost of data collection, some developing cities have few available data, which makes it infeasible to train a well-performed model. To address this challenge, cross-city knowledge transfer has shown its promise, where the model learned from data-sufficient cities is leveraged to benefit the learning process of data-scarce cities. However, the spatio-temporal graphs among different cities show irregular structures and varied features, which limits the feasibility of existing Few-Shot Learning (\emph{FSL}) methods. Therefore, we propose a model-agnostic few-shot learning framework for spatio-temporal graph called ST-GFSL. Specifically, to enhance feature extraction by transfering cross-city knowledge, ST-GFSL proposes to generate non-shared parameters based on node-level meta knowledge. The nodes in target city transfer the knowledge via parameter matching, retrieving from similar spatio-temporal characteristics. Furthermore, we propose to reconstruct the graph structure during meta-learning. The graph reconstruction loss is defined to guide structure-aware learning, avoiding structure deviation among different datasets. We conduct comprehensive experiments on four traffic speed prediction benchmarks and the results demonstrate the effectiveness of ST-GFSL compared with state-of-the-art methods.
Outstanding achievements of graph neural networks for spatiotemporal time series analysis show that relational constraints introduce an effective inductive bias into neural forecasting architectures. Often, however, the relational information characterizing the underlying data-generating process is unavailable and the practitioner is left with the problem of inferring from data which relational graph to use in the subsequent processing stages. We propose novel, principled - yet practical - probabilistic score-based methods that learn the relational dependencies as distributions over graphs while maximizing end-to-end the performance at task. The proposed graph learning framework is based on consolidated variance reduction techniques for Monte Carlo score-based gradient estimation, is theoretically grounded, and, as we show, effective in practice. In this paper, we focus on the time series forecasting problem and show that, by tailoring the gradient estimators to the graph learning problem, we are able to achieve state-of-the-art performance while controlling the sparsity of the learned graph and the computational scalability. We empirically assess the effectiveness of the proposed method on synthetic and real-world benchmarks, showing that the proposed solution can be used as a stand-alone graph identification procedure as well as a graph learning component of an end-to-end forecasting architecture.
Random walk kernels have been introduced in seminal work on graph learning and were later largely superseded by kernels based on the Weisfeiler-Leman test for graph isomorphism. We give a unified view on both classes of graph kernels. We study walk-based node refinement methods and formally relate them to several widely-used techniques, including Morgan's algorithm for molecule canonization and the Weisfeiler-Leman test. We define corresponding walk-based kernels on nodes that allow fine-grained parameterized neighborhood comparison, reach Weisfeiler-Leman expressiveness, and are computed using the kernel trick. From this we show that classical random walk kernels with only minor modifications regarding definition and computation are as expressive as the widely-used Weisfeiler-Leman subtree kernel but support non-strict neighborhood comparison. We verify experimentally that walk-based kernels reach or even surpass the accuracy of Weisfeiler-Leman kernels in real-world classification tasks.
Self-supervised learning (SSL) has been extensively explored in recent years. Particularly, generative SSL has seen emerging success in natural language processing and other AI fields, such as the wide adoption of BERT and GPT. Despite this, contrastive learning-which heavily relies on structural data augmentation and complicated training strategies-has been the dominant approach in graph SSL, while the progress of generative SSL on graphs, especially graph autoencoders (GAEs), has thus far not reached the potential as promised in other fields. In this paper, we identify and examine the issues that negatively impact the development of GAEs, including their reconstruction objective, training robustness, and error metric. We present a masked graph autoencoder GraphMAE that mitigates these issues for generative self-supervised graph pretraining. Instead of reconstructing graph structures, we propose to focus on feature reconstruction with both a masking strategy and scaled cosine error that benefit the robust training of GraphMAE. We conduct extensive experiments on 21 public datasets for three different graph learning tasks. The results manifest that GraphMAE-a simple graph autoencoder with careful designs-can consistently generate outperformance over both contrastive and generative state-of-the-art baselines. This study provides an understanding of graph autoencoders and demonstrates the potential of generative self-supervised pre-training on graphs.
Choices made by individuals have widespread impacts--for instance, people choose between political candidates to vote for, between social media posts to share, and between brands to purchase--moreover, data on these choices are increasingly abundant. Discrete choice models are a key tool for learning individual preferences from such data. Additionally, social factors like conformity and contagion influence individual choice. Traditional methods for incorporating these factors into choice models do not account for the entire social network and require hand-crafted features. To overcome these limitations, we use graph learning to study choice in networked contexts. We identify three ways in which graph learning techniques can be used for discrete choice: learning chooser representations, regularizing choice model parameters, and directly constructing predictions from a network. We design methods in each category and test them on real-world choice datasets, including county-level 2016 US election results and Android app installation and usage data. We show that incorporating social network structure can improve the predictions of the standard econometric choice model, the multinomial logit. We provide evidence that app installations are influenced by social context, but we find no such effect on app usage among the same participants, which instead is habit-driven. In the election data, we highlight the additional insights a discrete choice framework provides over classification or regression, the typical approaches. On synthetic data, we demonstrate the sample complexity benefit of using social information in choice models.
Graph Neural Networks (GNNs) have been predominant for graph learning tasks; however, recent studies showed that a well-known graph algorithm, Label Propagation (LP), combined with a shallow neural network can achieve comparable performance to GNNs in semi-supervised node classification on graphs with high homophily. In this paper, we show that this approach falls short on graphs with low homophily, where nodes often connect to the nodes of the opposite classes. To overcome this, we carefully design a combination of a base predictor with LP algorithm that enjoys a closed-form solution as well as convergence guarantees. Our algorithm first learns the class compatibility matrix and then aggregates label predictions using LP algorithm weighted by class compatibilities. On a wide variety of benchmarks, we show that our approach achieves the leading performance on graphs with various levels of homophily. Meanwhile, it has orders of magnitude fewer parameters and requires less execution time. Empirical evaluations demonstrate that simple adaptations of LP can be competitive in semi-supervised node classification in both homophily and heterophily regimes.
Graph neural networks (GNNs) mainly rely on the message-passing paradigm to propagate node features and build interactions, and different graph learning tasks require different ranges of node interactions. In this work, we explore the capacity of GNNs to capture interactions between nodes under contexts with different complexities. We discover that GNNs are usually unable to capture the most informative kinds of interaction styles for diverse graph learning tasks, and thus name this phenomenon as GNNs' representation bottleneck. As a response, we demonstrate that the inductive bias introduced by existing graph construction mechanisms can prevent GNNs from learning interactions of the most appropriate complexity, i.e., resulting in the representation bottleneck. To address that limitation, we propose a novel graph rewiring approach based on interaction patterns learned by GNNs to adjust the receptive fields of each node dynamically. Extensive experiments on both real-world and synthetic datasets prove the effectiveness of our algorithm to alleviate the representation bottleneck and its superiority to enhance the performance of GNNs over state-of-the-art graph rewiring baselines.
While hyper-parameters (HPs) are important for knowledge graph (KG) learning, existing methods fail to search them efficiently. To solve this problem, we first analyze the properties of different HPs and measure the transfer ability from small subgraph to the full graph. Based on the analysis, we propose an efficient two-stage search algorithm KGTuner, which efficiently explores HP configurations on small subgraph at the first stage and transfers the top-performed configurations for fine-tuning on the large full graph at the second stage. Experiments show that our method can consistently find better HPs than the baseline algorithms within the same time budget, which achieves {9.1\%} average relative improvement for four embedding models on the large-scale KGs in open graph benchmark.