Popular graph neural networks are shallow models, despite the success of very deep architectures in other application domains of deep learning. This reduces the modeling capacity and leaves models unable to capture long-range relationships. The primary reason for the shallow design results from over-smoothing, which leads node states to become more similar with increased depth. We build on the close connection between GNNs and PageRank, for which personalized PageRank introduces the consideration of a personalization vector. Adopting this idea, we propose the Personalized PageRank Graph Neural Network (PPRGNN), which extends the graph convolutional network to an infinite-depth model that has a chance to reset the neighbor aggregation back to the initial state in each iteration. We introduce a nicely interpretable tweak to the chance of resetting and prove the convergence of our approach to a unique solution without placing any constraints, even when taking infinitely many neighbor aggregations. As in personalized PageRank, our result does not suffer from over-smoothing. While doing so, time complexity remains linear while we keep memory complexity constant, independently of the depth of the network, making it scale well to large graphs. We empirically show the effectiveness of our approach for various node and graph classification tasks. PPRGNN outperforms comparable methods in almost all cases.
The problem of interpreting the decisions of machine learning is a well-researched and important. We are interested in a specific type of machine learning model that deals with graph data called graph neural networks. Evaluating interpretability approaches for graph neural networks (GNN) specifically are known to be challenging due to the lack of a commonly accepted benchmark. Given a GNN model, several interpretability approaches exist to explain GNN models with diverse (sometimes conflicting) evaluation methodologies. In this paper, we propose a benchmark for evaluating the explainability approaches for GNNs called Bagel. In Bagel, we firstly propose four diverse GNN explanation evaluation regimes -- 1) faithfulness, 2) sparsity, 3) correctness. and 4) plausibility. We reconcile multiple evaluation metrics in the existing literature and cover diverse notions for a holistic evaluation. Our graph datasets range from citation networks, document graphs, to graphs from molecules and proteins. We conduct an extensive empirical study on four GNN models and nine post-hoc explanation approaches for node and graph classification tasks. We open both the benchmarks and reference implementations and make them available at https://github.com/Mandeep-Rathee/Bagel-benchmark.
Following the success of convolution on non-Euclidean space, the corresponding pooling approaches have also been validated on various tasks regarding graphs. However, because of the fixed compression quota and stepwise pooling design, these hierarchical pooling methods still suffer from local structure damage and suboptimal problem. In this work, inspired by structural entropy, we propose a hierarchical pooling approach, SEP, to tackle the two issues. Specifically, without assigning the layer-specific compression quota, a global optimization algorithm is designed to generate the cluster assignment matrices for pooling at once. Then, we present an illustration of the local structure damage from previous methods in the reconstruction of ring and grid synthetic graphs. In addition to SEP, we further design two classification models, SEP-G and SEP-N for graph classification and node classification, respectively. The results show that SEP outperforms state-of-the-art graph pooling methods on graph classification benchmarks and obtains superior performance on node classifications.
We present a novel graph neural network we call AgentNet, which is designed specifically for graph-level tasks. AgentNet is inspired by sublinear algorithms, featuring a computational complexity that is independent of the graph size. The architecture of AgentNet differs fundamentally from the architectures of traditional graph neural networks. In AgentNet, some trained \textit{neural agents} intelligently walk the graph, and then collectively decide on the output. We provide an extensive theoretical analysis of AgentNet: We show that the agents can learn to systematically explore their neighborhood and that AgentNet can distinguish some structures that are even indistinguishable by 2-WL. Moreover, AgentNet is able to separate any two graphs which are sufficiently different in terms of subgraphs. We confirm these theoretical results with synthetic experiments on hard-to-distinguish graphs and real-world graph classification tasks. In both cases, we compare favorably not only to standard GNNs but also to computationally more expensive GNN extensions.
With the development of graph kernels and graph representation learning, many superior methods have been proposed to handle scalability and oversmoothing issues on graph structure learning. However, most of those strategies are designed based on practical experience rather than theoretical analysis. In this paper, we use a particular dummy node connecting to all existing vertices without affecting original vertex and edge properties. We further prove that such the dummy node can help build an efficient monomorphic edge-to-vertex transform and an epimorphic inverse to recover the original graph back. It also indicates that adding dummy nodes can preserve local and global structures for better graph representation learning. We extend graph kernels and graph neural networks with dummy nodes and conduct experiments on graph classification and subgraph isomorphism matching tasks. Empirical results demonstrate that taking graphs with dummy nodes as input significantly boosts graph structure learning, and using their edge-to-vertex graphs can also achieve similar results. We also discuss the gain of expressive power from the dummy in neural networks.
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.
Graph Neural Networks (GNNs) have been shown to achieve competitive results to tackle graph-related tasks, such as node and graph classification, link prediction and node and graph clustering in a variety of domains. Most GNNs use a message passing framework and hence are called MPNNs. Despite their promising results, MPNNs have been reported to suffer from over-smoothing, over-squashing and under-reaching. Graph rewiring and graph pooling have been proposed in the literature as solutions to address these limitations. However, most state-of-the-art graph rewiring methods fail to preserve the global topology of the graph, are neither differentiable nor inductive, and require the tuning of hyper-parameters. In this paper, we propose DiffWire, a novel framework for graph rewiring in MPNNs that is principled, fully differentiable and parameter-free by leveraging the Lov\'asz bound. The proposed approach provides a unified theory for graph rewiring by proposing two new, complementary layers in MPNNs: CT-Layer, a layer that learns the commute times and uses them as a relevance function for edge re-weighting; and GAP-Layer, a layer to optimize the spectral gap, depending on the nature of the network and the task at hand. We empirically validate the value of each of these layers separately with benchmark datasets for graph classification. We also perform preliminary studies on the use of CT-Layer for homophilic and heterophilic node classification tasks. DiffWire brings together the learnability of commute times to related definitions of curvature, opening the door to creating more expressive MPNNs.
Graph Neural Networks (GNNs) have been widely applied to various fields for learning over graph-structured data. They have shown significant improvements over traditional heuristic methods in various tasks such as node classification and graph classification. However, since GNNs heavily rely on smoothed node features rather than graph structure, they often show poor performance than simple heuristic methods in link prediction where the structural information, e.g., overlapped neighborhoods, degrees, and shortest paths, is crucial. To address this limitation, we propose Neighborhood Overlap-aware Graph Neural Networks (Neo-GNNs) that learn useful structural features from an adjacency matrix and estimate overlapped neighborhoods for link prediction. Our Neo-GNNs generalize neighborhood overlap-based heuristic methods and handle overlapped multi-hop neighborhoods. Our extensive experiments on Open Graph Benchmark datasets (OGB) demonstrate that Neo-GNNs consistently achieve state-of-the-art performance in link prediction. Our code is publicly available at https://github.com/seongjunyun/Neo_GNNs.
Many modern deep-learning techniques do not work without enormous datasets. At the same time, several fields demand methods working in scarcity of data. This problem is even more complex when the samples have varying structures, as in the case of graphs. Graph representation learning techniques have recently proven successful in a variety of domains. Nevertheless, the employed architectures perform miserably when faced with data scarcity. On the other hand, few-shot learning allows employing modern deep learning models in scarce data regimes without waiving their effectiveness. In this work, we tackle the problem of few-shot graph classification, showing that equipping a simple distance metric learning baseline with a state-of-the-art graph embedder allows to obtain competitive results on the task. While the simplicity of the architecture is enough to outperform more complex ones, it also allows straightforward additions. To this end, we show that additional improvements may be obtained by encouraging a task-conditioned embedding space. Finally, we propose a MixUp-based online data augmentation technique acting in the latent space and show its effectiveness on the task.
In deep neural networks, better results can often be obtained by increasing the complexity of previously developed basic models. However, it is unclear whether there is a way to boost performance by decreasing the complexity of such models. Intuitively, given a problem, a simpler data structure comes with a simpler algorithm. Here, we investigate the feasibility of improving graph classification performance while simplifying the learning process. Inspired by structural entropy on graphs, we transform the data sample from graphs to coding trees, which is a simpler but essential structure for graph data. Furthermore, we propose a novel message passing scheme, termed hierarchical reporting, in which features are transferred from leaf nodes to root nodes by following the hierarchical structure of coding trees. We then present a tree kernel and a convolutional network to implement our scheme for graph classification. With the designed message passing scheme, the tree kernel and convolutional network have a lower runtime complexity of $O(n)$ than Weisfeiler-Lehman subtree kernel and other graph neural networks of at least $O(hm)$. We empirically validate our methods with several graph classification benchmarks and demonstrate that they achieve better performance and lower computational consumption than competing approaches.
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.
Most graph neural network models rely on a particular message passing paradigm, where the idea is to iteratively propagate node representations of a graph to each node in the direct neighborhood. While very prominent, this paradigm leads to information propagation bottlenecks, as information is repeatedly compressed at intermediary node representations, which causes loss of information, making it practically impossible to gather meaningful signals from distant nodes. To address this, we propose shortest path message passing neural networks, where the node representations of a graph are propagated to each node in the shortest path neighborhoods. In this setting, nodes can directly communicate between each other even if they are not neighbors, breaking the information bottleneck and hence leading to more adequately learned representations. Our framework generalizes message passing neural networks, resulting in a class of more expressive models, including some recent state-of-the-art models. We verify the capacity of a basic model of this framework on dedicated synthetic experiments, and on real-world graph classification and regression benchmarks, and obtain state-of-the art results.
Graph kernels are conventional methods for computing graph similarities. However, the existing R-convolution graph kernels cannot resolve both of the two challenges: 1) Comparing graphs at multiple different scales, and 2) Considering the distributions of substructures when computing the kernel matrix. These two challenges limit their performances. To mitigate both of the two challenges, we propose a novel graph kernel called the Multi-scale Wasserstein Shortest-Path graph kernel (MWSP), at the heart of which is the multi-scale shortest-path node feature map, of which each element denotes the number of occurrences of the shortest path around a node. The shortest path is represented by the concatenation of all the labels of nodes in it. Since the shortest-path node feature map can only compare graphs at local scales, we incorporate into it the multiple different scales of the graph structure, which are captured by the truncated BFS trees of different depths rooted at each node in a graph. We use the Wasserstein distance to compute the similarity between the multi-scale shortest-path node feature maps of two graphs, considering the distributions of shortest paths. We empirically validate MWSP on various benchmark graph datasets and demonstrate that it achieves state-of-the-art performance on most datasets.
Current Graph Neural Networks (GNN) architectures generally rely on two important components: node features embedding through message passing, and aggregation with a specialized form of pooling. The structural (or topological) information is implicitly taken into account in these two steps. We propose in this work a novel point of view, which places distances to some learnable graph templates at the core of the graph representation. This distance embedding is constructed thanks to an optimal transport distance: the Fused Gromov-Wasserstein (FGW) distance, which encodes simultaneously feature and structure dissimilarities by solving a soft graph-matching problem. We postulate that the vector of FGW distances to a set of template graphs has a strong discriminative power, which is then fed to a non-linear classifier for final predictions. Distance embedding can be seen as a new layer, and can leverage on existing message passing techniques to promote sensible feature representations. Interestingly enough, in our work the optimal set of template graphs is also learnt in an end-to-end fashion by differentiating through this layer. After describing the corresponding learning procedure, we empirically validate our claim on several synthetic and real life graph classification datasets, where our method is competitive or surpasses kernel and GNN state-of-the-art approaches. We complete our experiments by an ablation study and a sensitivity analysis to parameters.
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.
Graph similarity learning refers to calculating the similarity score between two graphs, which is required in many realistic applications, such as visual tracking, graph classification, and collaborative filtering. As most of the existing graph neural networks yield effective graph representations of a single graph, little effort has been made for jointly learning two graph representations and calculating their similarity score. In addition, existing unsupervised graph similarity learning methods are mainly clustering-based, which ignores the valuable information embodied in graph pairs. To this end, we propose a contrastive graph matching network (CGMN) for self-supervised graph similarity learning in order to calculate the similarity between any two input graph objects. Specifically, we generate two augmented views for each graph in a pair respectively. Then, we employ two strategies, namely cross-view interaction and cross-graph interaction, for effective node representation learning. The former is resorted to strengthen the consistency of node representations in two views. The latter is utilized to identify node differences between different graphs. Finally, we transform node representations into graph-level representations via pooling operations for graph similarity computation. We have evaluated CGMN on eight real-world datasets, and the experiment results show that the proposed new approach is superior to the state-of-the-art methods in graph similarity learning downstream tasks.
We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being $\textit{local}$, $\textit{global}$ or $\textit{relative}$. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges $O(N+E)$ by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework $\textit{GraphGPS}$ that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.
Deep graph neural networks (GNNs) have been shown to be expressive for modeling graph-structured data. Nevertheless, the over-stacked architecture of deep graph models makes it difficult to deploy and rapidly test on mobile or embedded systems. To compress over-stacked GNNs, knowledge distillation via a teacher-student architecture turns out to be an effective technique, where the key step is to measure the discrepancy between teacher and student networks with predefined distance functions. However, using the same distance for graphs of various structures may be unfit, and the optimal distance formulation is hard to determine. To tackle these problems, we propose a novel Adversarial Knowledge Distillation framework for graph models named GraphAKD, which adversarially trains a discriminator and a generator to adaptively detect and decrease the discrepancy. Specifically, noticing that the well-captured inter-node and inter-class correlations favor the success of deep GNNs, we propose to criticize the inherited knowledge from node-level and class-level views with a trainable discriminator. The discriminator distinguishes between teacher knowledge and what the student inherits, while the student GNN works as a generator and aims to fool the discriminator. To our best knowledge, GraphAKD is the first to introduce adversarial training to knowledge distillation in graph domains. Experiments on node-level and graph-level classification benchmarks demonstrate that GraphAKD improves the student performance by a large margin. The results imply that GraphAKD can precisely transfer knowledge from a complicated teacher GNN to a compact student GNN.
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.
Due to the superior performance of Graph Neural Networks (GNNs) in various domains, there is an increasing interest in the GNN explanation problem "\emph{which fraction of the input graph is the most crucial to decide the model's decision?}" Existing explanation methods focus on the supervised settings, \eg, node classification and graph classification, while the explanation for unsupervised graph-level representation learning is still unexplored. The opaqueness of the graph representations may lead to unexpected risks when deployed for high-stake decision-making scenarios. In this paper, we advance the Information Bottleneck principle (IB) to tackle the proposed explanation problem for unsupervised graph representations, which leads to a novel principle, \textit{Unsupervised Subgraph Information Bottleneck} (USIB). We also theoretically analyze the connection between graph representations and explanatory subgraphs on the label space, which reveals that the expressiveness and robustness of representations benefit the fidelity of explanatory subgraphs. Experimental results on both synthetic and real-world datasets demonstrate the superiority of our developed explainer and the validity of our theoretical analysis.