ICML 2024 论文列表

The increasing amount of graph data places requirements on the efficient training of graph neural networks (GNNs). The emerging graph distillation (GD) tackles this challenge by distilling a small synthetic graph to replace the real large graph, ensuring GNNs trained on real and synthetic graphs exhibit comparable performance. However, existing methods rely on GNN-related information as supervision, including gradients, representations, and trajectories, which have two limitations. First, GNNs can affect the spectrum (*i.e*., eigenvalues) of the real graph, causing *spectrum bias* in the synthetic graph. Second, the variety of GNN architectures leads to the creation of different synthetic graphs, requiring *traversal* to obtain optimal performance. To tackle these issues, we propose Graph Distillation with Eigenbasis Matching (GDEM), which aligns the eigenbasis and node features of real and synthetic graphs. Meanwhile, it directly replicates the spectrum of the real graph and thus prevents the influence of GNNs. Moreover, we design a discrimination constraint to balance the effectiveness and generalization of GDEM. Theoretically, the synthetic graphs distilled by GDEM are restricted spectral approximations of the real graphs. Extensive experiments demonstrate that GDEM outperforms state-of-the-art GD methods with powerful cross-architecture generalization ability and significant distillation efficiency. Our code is available at https://github.com/liuyang-tian/GDEM.

Much of the world's most valued data is stored in relational databases and data warehouses, where the data is organized into tables connected by primary-foreign key relations. However, building machine learning models using this data is both challenging and time consuming because no ML algorithm can directly learn from multiple connected tables. Current approaches can only learn from a single table, so data must first be manually joined and aggregated into this format, the laborious process known as feature engineering. Feature engineering is slow, error prone and leads to suboptimal models. Here we introduce Relational Deep Learning (RDL), a blueprint for end-to-end learning on relational databases. The key is to represent relational databases as a temporal, heterogeneous graphs, with a node for each row in each table, and edges specified by primary-foreign key links. Graph Neural Networks then learn representations that leverage all input data, without any manual feature engineering. We also introduce RelBench, and benchmark and testing suite, demonstrating strong initial results. Overall, we define a new research area that generalizes graph machine learning and broadens its applicability.

We propose Unsupervised Episode Generation method called **Neighbors as Queries (NaQ)** to solve the Few-Shot Node-Classification (FSNC) task by *unsupervised Graph Meta-learning*. Doing so enables full utilization of the information of all nodes in a graph, which is not possible in current supervised meta-learning methods for FSNC due to the label-scarcity problem. In addition, unlike unsupervised Graph Contrastive Learning (GCL) methods that overlook the downstream task to be solved at the training phase resulting in vulnerability to class imbalance of a graph, we adopt the episodic learning framework that allows the model to be aware of the downstream task format, i.e., FSNC. The proposed NaQ is a simple but effective *unsupervised* episode generation method that randomly samples nodes from a graph to make a support set, followed by similarity-based sampling of nodes to make the corresponding query set. Since NaQ is *model-agnostic*, any existing supervised graph meta-learning methods can be trained in an unsupervised manner, while not sacrificing much of their performance or sometimes even improving them. Extensive experimental results demonstrate the effectiveness of our proposed unsupervised episode generation method for graph meta-learning towards the FSNC task. Our code is available at: https://github.com/JhngJng/NaQ-PyTorch.

Two-stage Stochastic Programming (2SP) is a standard framework for modeling decision-making problems under uncertainty. While numerous methods exist, solving such problems with many scenarios remains challenging. Selecting representative scenarios is a practical method for accelerating solutions. However, current approaches typically rely on clustering or Monte Carlo sampling, failing to integrate scenario information deeply and overlooking the significant impact of the scenario order on solving time. To address these issues, we develop HGCN2SP, a novel model with a hierarchical graph designed for 2SP problems, encoding each scenario and modeling their relationships hierarchically. The model is trained in a reinforcement learning paradigm to utilize the feedback of the solver. The policy network is equipped with a hierarchical graph convolutional network for feature encoding and an attention-based decoder for scenario selection in proper order. Evaluation of two classic 2SP problems demonstrates that HGCN2SP provides high-quality decisions in a short computational time. Furthermore, HGCN2SP exhibits remarkable generalization capabilities in handling large-scale instances, even with a substantial number of variables or scenarios that were unseen during the training phase.

This work provides a theoretical framework for assessing the generalization error of graph neural networks in the over-parameterized regime, where the number of parameters surpasses the quantity of data points. We explore two widely utilized types of graph neural networks: graph convolutional neural networks and message passing graph neural networks. Prior to this study, existing bounds on the generalization error in the over-parametrized regime were uninformative, limiting our understanding of over-parameterized network performance. Our novel approach involves deriving upper bounds within the mean-field regime for evaluating the generalization error of these graph neural networks. We establish upper bounds with a convergence rate of $O(1/n)$, where $n$ is the number of graph samples. These upper bounds offer a theoretical assurance of the networks' performance on unseen data in the challenging over-parameterized regime and overall contribute to our understanding of their performance.

In this paper, we consider classic randomized low diameter decomposition procedures for planar graphs that obtain connected clusters that are cohesive in that close by pairs of nodes are assigned to the same cluster with high probability. We consider the additional aspect of *individual fairness* -- pairs of nodes at comparable distances should be separated with comparable probability. We show that classic decomposition procedures do not satisfy this property. We present novel algorithms that achieve various trade-offs between this property and additional desiderata of connectivity of the clusters and optimality in number of clusters. We show that our individual fairness bounds may be difficult to improve by tying the improvement to resolving a major open question in metric embeddings. We finally show the efficacy of our algorithms on real planar networks modeling Congressional redistricting.

Graph neural networks based on iterative one-hop message passing have been shown to struggle in harnessing the information from distant nodes effectively. Conversely, graph transformers allow each node to attend to all other nodes directly, but lack graph inductive bias and have to rely on ad-hoc positional encoding. In this paper, we propose a new architecture to reconcile these challenges. Our approach stems from the recent breakthroughs in long-range modeling provided by deep state-space models: for a given target node, our model aggregates other nodes by their shortest distances to the target and uses a linear RNN to encode the sequence of hop representations. The linear RNN is parameterized in a particular diagonal form for stable long-range signal propagation and is theoretically expressive enough to encode the neighborhood hierarchy. With no need for positional encoding, we empirically show that the performance of our model is comparable to or better than that of state-of-the-art graph transformers on various benchmarks, with a significantly reduced computational cost. Our code is open-source at https://github.com/skeletondyh/GRED.

Most real-world networks are noisy and incomplete samples from an unknown target distribution. Refining them by correcting corruptions or inferring unobserved regions typically improves downstream performance. Inspired by the impressive generative capabilities that have been used to correct corruptions in images, and the similarities between "in-painting" and filling in missing nodes and edges conditioned on the observed graph, we propose a novel graph generative framework, SGDM, which is based on subgraph diffusion. Our framework not only improves the scalability and fidelity of graph diffusion models, but also leverages the reverse process to perform novel, conditional generation tasks. In particular, through extensive empirical analysis and a set of novel metrics, we demonstrate that our proposed model effectively supports the following refinement tasks for partially observable networks: (T1) denoising extraneous subgraphs, (T2) expanding existing subgraphs and (T3) performing ``style" transfer by regenerating a particular subgraph to match the characteristics of a different node or subgraph.

The Shapley value is a prominent tool for interpreting black-box machine learning models thanks to its strong theoretical foundation. However, for models with structured inputs, such as graph neural networks, existing Shapley-based explainability approaches either focus solely on node-wise importance or neglect the graph structure when perturbing the input instance. This paper introduces the Myerson-Taylor interaction index that internalizes the graph structure into attributing the node values and the interaction values among nodes. Unlike the Shapley-based methods, the Myerson-Taylor index decomposes coalitions into components satisfying a pre-chosen connectivity criterion. We prove that the Myerson-Taylor index is the unique one that satisfies a system of five natural axioms accounting for graph structure and high-order interaction among nodes. Leveraging these properties, we propose Myerson-Taylor Structure-Aware Graph Explainer (MAGE), a novel explainer that uses the second-order Myerson-Taylor index to identify the most important motifs influencing the model prediction, both positively and negatively. Extensive experiments on various graph datasets and models demonstrate that our method consistently provides superior subgraph explanations compared to state-of-the-art methods.

Predicting the binding sites of target proteins plays a fundamental role in drug discovery. Most existing deep-learning methods consider a protein as a 3D image by spatially clustering its atoms into voxels and then feed the voxelized protein into a 3D CNN for prediction. However, the CNN-based methods encounter several critical issues: 1) defective in representing irregular protein structures; 2) sensitive to rotations; 3) insufficient to characterize the protein surface; 4) unaware of protein size shift. To address the above issues, this work proposes EquiPocket, an E(3)-equivariant Graph Neural Network (GNN) for binding site prediction, which comprises three modules: the first one to extract local geometric information for each surface atom, the second one to model both the chemical and spatial structure of protein and the last one to capture the geometry of the surface via equivariant message passing over the surface atoms. We further propose a dense attention output layer to alleviate the effect incurred by variable protein size. Extensive experiments on several representative benchmarks demonstrate the superiority of our framework to the state-of-the-art methods.

The Transformer architecture has recently gained considerable attention in the field of graph representation learning, as it naturally overcomes several limitations of Graph Neural Networks (GNNs) with customized attention mechanisms or positional and structural encodings. Despite making some progress, existing works tend to overlook external information of graphs, specifically the correlation between graphs. Intuitively, graphs with similar structures should have similar representations. Therefore, we propose Graph External Attention (GEA) --- a novel attention mechanism that leverages multiple external node/edge key-value units to capture inter-graph correlations implicitly. On this basis, we design an effective architecture called Graph External Attention Enhanced Transformer (GEAET), which integrates local structure and global interaction information for more comprehensive graph representations. Extensive experiments on benchmark datasets demonstrate that GEAET achieves state-of-the-art empirical performance. The source code is available for reproducibility at: https://github.com/icm1018/GEAET.

We investigate the trade-off between the representation power of graph generative models and model *overlap*, i.e., the degree to which the model generates diverse outputs versus regurgitating its training data. In particular, we delineate a nested hierarchy of graph generative models categorized into three levels of complexity: edge independent, node independent, and arbitrarily dependent models. This hierarchy encapsulates a wide range of prevalent methods. We derive theoretical bounds on the number of triangles and other short-length cycles producible by each level of the hierarchy, finding that more complex dependency structure allows an improved trade-off between representation power and overlap. We provide instances demonstrating the asymptotic optimality of our bounds. Furthermore, we introduce new generative models for each of the three hierarchical levels, leveraging dense subgraph discovery. Our evaluation, conducted on real-world datasets, focuses on assessing the output quality and overlap of our proposed models in comparison to other popular models. Our results indicate that our simple, interpretable models provide competitive baselines to popular generative models. Through this investigation, we offer a structured and robust evaluation scheme, thereby facilitating the development of models capable of generating accurate and edge-diverse graphs.

Graph neural networks (GNNs) have exhibited superb power in many graph related tasks. Existing GNNs can be categorized into spatial GNNs and spectral GNNs. The spatial GNNs primarily capture the local information around each node, while the spectral GNNs are able to operate on the frequency signals of the entire graph. However, most, if not all, existing spectral GNNs are faced with two limitations: (1) the polynomial limitation that for most spectral GNNs, the expressive power in the spectral domain is limited to polynomial filters; and (2) the transductive limitation that most spectral GNNs can only be applied to the transductive setting on relatively small-scale graphs. In this paper, we propose a novel spectral graph neural network named SLOG to solve the above two limitations. For the polynomial limitation, SLOG proposes a novel real-valued filter with geometric interpretability, mathematical feasibility and adaptive filtering ability to go beyond polynomial. For the transductive limitation, SLOG combines the subgraph sampling technique in spatial GNNs and the signal processing technique in spectral GNNs together to make itself tailored to the inductive setting on large-scale graphs. Extensive experimental results on 16 datasets demonstrate the superiority of SLOG in inductive homophilic and heterophilic node classification task.

Although most graph neural networks (GNNs) can operate on graphs of any size, their classification performance often declines on graphs larger than those encountered during training. Existing methods insufficiently address the removal of size information from graph representations, resulting in sub-optimal performance and reliance on backbone models. In response, we propose DISGEN, a novel and model-agnostic framework designed to disentangle size factors from graph representations. DISGEN employs size- and task-invariant augmentations and introduces a decoupling loss that minimizes shared information in hidden representations, with theoretical guarantees for its effectiveness. Our empirical results show that DISGEN outperforms the state-of-the-art models by up to 6% on real-world datasets, underscoring its effectiveness in enhancing the size generalizability of GNNs. Our codes are available at: https://github.com/GraphmindDartmouth/DISGEN.

We study the optimal transport (OT) problem for measures supported on a graph metric space. Recently, Le et al. (2022) leverage the graph structure and propose a variant of OT, namely Sobolev transport (ST), which yields a closed-form expression for a fast computation. However, ST is essentially coupled with the $L^p$ geometric structure within its definition which makes it nontrivial to utilize ST for other prior structures. In contrast, the classic OT has the flexibility to adapt to various geometric structures by modifying the underlying cost function. An important instance is the Orlicz-Wasserstein (OW) which moves beyond the $L^p$ structure by leveraging the *Orlicz geometric structure*. Comparing to the usage of standard $p$-order Wasserstein, OW remarkably helps to advance certain machine learning approaches. Nevertheless, OW brings up a new challenge on its computation due to its two-level optimization formulation. In this work, we leverage a specific class of convex functions for Orlicz structure to propose the generalized Sobolev transport (GST). GST encompasses the ST as its special case, and can be utilized for prior structures beyond the $L^p$ geometry. In connection with the OW, we show that one only needs to simply solve a univariate optimization problem to compute the GST, unlike the complex two-level optimization problem in OW. We empirically illustrate that GST is several-order faster than the OW. Moreover, we provide preliminary evidences on the advantages of GST for document classification and for several tasks in topological data analysis.