ICML 2023 Papers

Despite the widespread use of graph neural networks (GNNs) we lack methods to reliably quantify their uncertainty. We propose a conformal procedure to equip GNNs with prediction sets that come with distribution-free guarantees -- the output set contains the true label with arbitrarily high probability. Our post-processing procedure can wrap around any (pretrained) GNN, and unlike existing methods, results in meaningful sets even when the model provides only the top class. The key idea is to diffuse the node-wise conformity scores to incorporate neighborhood information. By leveraging the network homophily we construct sets with comparable or better efficiency (average size) and significantly improved singleton hit ratio (correct sets of size one). In addition to an extensive empirical evaluation, we investigate the theoretical conditions under which smoothing provably improves efficiency.

Graph Neural Networks (GNNs) are popular models for graph learning problems. GNNs show strong empirical performance in many practical tasks. However, the theoretical properties have not been completely elucidated. In this paper, we investigate whether GNNs can exploit the graph structure from the perspective of the expressive power of GNNs. In our analysis, we consider graph generation processes that are controlled by hidden (or latent) node features, which contain all information about the graph structure. A typical example of this framework is kNN graphs constructed from the hidden features. In our main results, we show that GNNs can recover the hidden node features from the input graph alone, even when all node features, including the hidden features themselves and any indirect hints, are unavailable. GNNs can further use the recovered node features for downstream tasks. These results show that GNNs can fully exploit the graph structure by themselves, and in effect, GNNs can use both the hidden and explicit node features for downstream tasks. In the experiments, we confirm the validity of our results by showing that GNNs can accurately recover the hidden features using a GNN architecture built based on our theoretical analysis.

We introduce a randomized topological augmentor based on Schur complements for Graph Contrastive Learning (GCL). Given a graph laplacian matrix, the technique generates unbiased approximations of its Schur complements and treats the corresponding graphs as augmented views. We discuss the benefits of our approach, provide theoretical justifications and present connections with graph diffusion. Unlike previous efforts, we study the empirical effectiveness of the augmentor in a controlled fashion by varying the design choices for subsequent GCL phases, such as encoding and contrasting. Extensive experiments on node and graph classification benchmarks demonstrate that our technique consistently outperforms pre-defined and adaptive augmentation approaches to achieve state-of-the-art results.

Graph coarsening is a dimensionality reduction technique that aims to learn a smaller-tractable graph while preserving the properties of the original input graph. However, many real-world graphs also have features or contexts associated with each node. The existing graph coarsening methods do not consider the node features and rely solely on a graph matrix(e.g., adjacency and Laplacian) to coarsen graphs. However, some recent deep learning-based graph coarsening methods are designed for specific tasks considering both node features and graph matrix. In this paper, we introduce a novel optimization-based framework for graph coarsening that takes both the graph matrix and the node features as the input and jointly learns the coarsened graph matrix and the coarsened feature matrix while ensuring desired properties. To the best of our knowledge, this is the first work that guarantees that the learned coarsened graph is $\epsilon\in[0,1)$ similar to the original graph. Extensive experiments with both real and synthetic benchmark datasets elucidate the proposed framework's efficacy and applicability for numerous graph-based applications, including graph clustering, node classification, stochastic block model identification, and graph summarization.

Dictionary learning, which approximates data samples by a set of shared atoms, is a fundamental task in representation learning. However, dictionary learning over graphs, namely graph dictionary learning (GDL), is much more challenging than vectorial data as graphs lie in disparate metric spaces. The sparse literature on GDL formulates the problem from the reconstructive view and often learns linear graph embeddings with a high computational cost. In this paper, we propose a Fused Gromov-Wasserstein (FGW) Mixture Model named FraMe to address the GDL problem from the generative view. Equipped with the graph generation function based on the radial basis function kernel and FGW distance, FraMe generates nonlinear embedding spaces, which, as we theoretically proved, provide a good approximation of the original graph spaces. A fast solution is further proposed on top of the expectation-maximization algorithm with guaranteed convergence. Extensive experiments demonstrate the effectiveness of the obtained node and graph embeddings, and our algorithm achieves significant improvements over the state-of-the-art methods.

The latest two-stage optimization framework based on graph neural network (GNN) and large neighborhood search (LNS) is the most popular framework in solving large-scale integer programs (IPs). However, the framework can not effectively use the embedding spatial information in GNN and still highly relies on large-scale solvers in LNS, resulting in the scale of IP being limited by the ability of the current solver and performance bottlenecks. To handle these issues, this paper presents a GNN&GBDT-guided fast optimizing framework for large-scale IPs that only uses a small-scale optimizer to solve large-scale IPs efficiently. Specifically, the proposed framework can be divided into three stages: Multi-task GNN Embedding to generate the embedding space, GBDT Prediction to effectively use the embedding spatial information, and Neighborhood Optimization to solve large-scale problems fast using the small-scale optimizer. Extensive experiments show that the proposed framework can solve IPs with millions of scales and surpass SCIP and Gurobi in the specified wall-clock time using only a small-scale optimizer with 30% of the problem size. It also shows that the proposed framework can save 99% of running time in achieving the same solution quality as SCIP, which verifies the effectiveness and efficiency of the proposed framework in solving large-scale IPs.

In recent years, there has been a significant amount of research focused on expanding the expressivity of Graph Neural Networks (GNNs) beyond the Weisfeiler-Lehman (1-WL) framework. While many of these studies have yielded advancements in expressivity, they have frequently come at the expense of decreased efficiency or have been restricted to specific types of graphs. In this study, we investigate the expressivity of GNNs from the perspective of graph search. Specifically, we propose a new vertex colouring scheme and demonstrate that classical search algorithms can efficiently compute graph representations that extend beyond the 1-WL. We show the colouring scheme inherits useful properties from graph search that can help solve problems like graph biconnectivity. Furthermore, we show that under certain conditions, the expressivity of GNNs increases hierarchically with the radius of the search neighbourhood. To further investigate the proposed scheme, we develop a new type of GNN based on two search strategies, breadth-first search and depth-first search, highlighting the graph properties they can capture on top of 1-WL. Our code is available at https://github.com/seanli3/lvc.

Dynamical systems with complex behaviours, e.g. immune system cells interacting with a pathogen, are commonly modelled by splitting the behaviour in different regimes, or *modes*, each with simpler dynamics, and then learn the switching behaviour from one mode to another. To achieve this, Switching Dynamical Systems (SDS) are a powerful tool that automatically discovers these modes and mode-switching behaviour from time series data. While effective, these methods focus on *independent objects*, where the modes of one object are independent of the modes of the other objects. In this paper, we focus on the more general *interacting object* setting for switching dynamical systems, where the per-object dynamics also depend on an unknown and dynamically changing subset of other objects and their modes. To this end, we propose a novel graph-based approach for switching dynamical systems, GRAph Switching dynamical Systems (GRASS), in which we use a dynamic graph to characterize interactions between objects and learn both intra-object and inter-object mode-switching behaviour. For benchmarking, we create two new datasets, a synthesized ODE-driven particles dataset and a real-world Salsa-couple dancing dataset. Experiments show that GRASS can consistently outperforms previous state-of-the-art methods. We will release code and data after acceptance.

Neural architecture search (NAS) for Graph neural networks (GNNs), called NAS-GNNs, has achieved significant performance over manually designed GNN architectures. However, these methods inherit issues from the conventional NAS methods, such as high computational cost and optimization difficulty. More importantly, previous NAS methods have ignored the uniqueness of GNNs, where GNNs possess expressive power without training. With the randomly-initialized weights, we can then seek the optimal architecture parameters via the sparse coding objective and derive a novel NAS-GNNs method, namely neural architecture coding (NAC). Consequently, our NAC holds a no-update scheme on GNNs and can efficiently compute in linear time. Empirical evaluations on multiple GNN benchmark datasets demonstrate that our approach leads to state-of-the-art performance, which is up to $200\times$ faster and $18.8\%$ more accurate than the strong baselines.

We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lovász' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.

In contrastive learning, the choice of "view" controls the information that the representation captures and influences the performance of the model. However, leading graph contrastive learning methods generally produce views via random corruption or learning, which could lead to the loss of essential information and alteration of semantic information. An anchor view that maintains the essential information of input graphs for contrastive learning has been hardly investigated. In this paper, based on the theory of graph information bottleneck, we deduce the definition of this anchor view; put differently, the anchor view with essential information of input graph is supposed to have the minimal structural uncertainty. Furthermore, guided by structural entropy, we implement the anchor view, termed SEGA, for graph contrastive learning. We extensively validate the proposed anchor view on various benchmarks regarding graph classification under unsupervised, semi-supervised, and transfer learning and achieve significant performance boosts compared to the state-of-the-art methods.

Graph Neural Networks (GNN) are inherently limited in their expressive power. Recent seminal works (Xu et al., 2019; Morris et al., 2019b) introduced the Weisfeiler-Lehman (WL) hierarchy as a measure of expressive power. Although this hierarchy has propelled significant advances in GNN analysis and architecture developments, it suffers from several significant limitations. These include a complex definition that lacks direct guidance for model improvement and a WL hierarchy that is too coarse to study current GNNs. This paper introduces an alternative expressive power hierarchy based on the ability of GNNs to calculate equivariant polynomials of a certain degree. As a first step, we provide a full characterization of all equivariant graph polynomials by introducing a concrete basis, significantly generalizing previous results. Each basis element corresponds to a specific multi-graph, and its computation over some graph data input corresponds to a tensor contraction problem. Second, we propose algorithmic tools for evaluating the expressiveness of GNNs using tensor contraction sequences, and calculate the expressive power of popular GNNs. Finally, we enhance the expressivity of common GNN architectures by adding polynomial features or additional operations / aggregations inspired by our theory. These enhanced GNNs demonstrate state-of-the-art results in experiments across multiple graph learning benchmarks.

Unsupervised multiplex graph representation learning (UMGRL) has received increasing interest, but few works simultaneously focused on the common and private information extraction. In this paper, we argue that it is essential for conducting effective and robust UMGRL to extract complete and clean common information, as well as more-complementarity and less-noise private information. To achieve this, we first investigate disentangled representation learning for the multiplex graph to capture complete and clean common information, as well as design a contrastive constraint to preserve the complementarity and remove the noise in the private information. Moreover, we theoretically analyze that the common and private representations learned by our method are provably disentangled and contain more task-relevant and less task-irrelevant information to benefit downstream tasks. Extensive experiments verify the superiority of the proposed method in terms of different downstream tasks.

Message passing neural networks have shown a lot of success on graph-structured data. However, there are many instances where message passing can lead to over-smoothing or fail when neighboring nodes belong to different classes. In this work, we introduce a simple yet general framework for improving learning in message passing neural networks. Our approach essentially upsamples edges in the original graph by adding "slow nodes" at each edge that can mediate communication between a source and a target node. Our method only modifies the input graph, making it plug-and-play and easy to use with existing models. To understand the benefits of slowing down message passing, we provide theoretical and empirical analyses. We report results on several supervised and self-supervised benchmarks, and show improvements across the board, notably in heterophilic conditions where adjacent nodes are more likely to have different labels. Finally, we show how our approach can be used to generate augmentations for self-supervised learning, where slow nodes are randomly introduced into different edges in the graph to generate multi-scale views with variable path lengths.

This paper develops an approximation to the (effective) $p$-resistance and applies it to multi-class clustering. Spectral methods based on the graph Laplacian and its generalization to the graph $p$-Laplacian have been a backbone of non-euclidean clustering techniques. The advantage of the $p$-Laplacian is that the parameter $p$ induces a controllable bias on cluster structure. The drawback of $p$-Laplacian eigenvector based methods is that the third and higher eigenvectors are difficult to compute. Thus, instead, we are motivated to use the $p$-resistance induced by the $p$-Laplacian for clustering. For $p$-resistance, small $p$ biases towards clusters with high internal connectivity while large $p$ biases towards clusters of small ``extent,'' that is a preference for smaller shortest-path distances between vertices in the cluster. However, the $p$-resistance is expensive to compute. We overcome this by developing an approximation to the $p$-resistance. We prove upper and lower bounds on this approximation and observe that it is exact when the graph is a tree. We also provide theoretical justification for the use of $p$-resistance for clustering. Finally, we provide experiments comparing our approximated $p$-resistance clustering to other $p$-Laplacian based methods.

Domain decomposition methods (DDMs) are popular solvers for discretized systems of partial differential equations (PDEs), with one-level and multilevel variants. These solvers rely on several algorithmic and mathematical parameters, prescribing overlap, subdomain boundary conditions, and other properties of the DDM. While some work has been done on optimizing these parameters, it has mostly focused on the one-level setting or special cases such as structured-grid discretizations with regular subdomain construction. In this paper, we propose multigrid graph neural networks (MG-GNN), a novel GNN architecture for learning optimized parameters in two-level DDMs. We train MG-GNN using a new unsupervised loss function, enabling effective training on small problems that yields robust performance on unstructured grids that are orders of magnitude larger than those in the training set. We show that MG-GNN outperforms popular hierarchical graph network architectures for this optimization and that our proposed loss function is critical to achieving this improved performance.

Graph neural networks aim to learn representations for graph-structured data and show impressive performance in node classification. Recently, many methods have studied the representations of GNNs from the perspective of optimization goals and spectral graph theory. However, the feature space that dominates representation learning has not been systematically studied in graph neural networks. In this paper, we propose to fill this gap by analyzing the feature space of both spatial and spectral models. We decompose graph neural networks into determined feature spaces and trainable weights, providing the convenience of studying the feature space explicitly using matrix space analysis. In particular, we find theoretically that the feature space tends to be linearly correlated due to repeated aggregations. In this case, the feature space is bounded by the poor representation of shared weights or the limited dimensionality of node attributes in existing models, leading to poor performance. Motivated by these findings, we propose 1) feature subspaces flattening and 2) structural principal components to expand the feature space. Extensive experiments verify the effectiveness of our proposed more comprehensive feature space, with comparable inference time to the baseline, and demonstrate its efficient convergence capability.

We present two new classes of algorithms for efficient field integration on graphs encoding point cloud data. The first class, $\mathrm{SeparatorFactorization}$ (SF), leverages the bounded genus of point cloud mesh graphs, while the second class, $\mathrm{RFDiffusion}$ (RFD), uses popular $\epsilon$-nearest-neighbor graph representations for point clouds. Both can be viewed as providing the functionality of Fast Multipole Methods (FMMs), which have had a tremendous impact on efficient integration, but for non-Euclidean spaces. We focus on geometries induced by distributions of walk lengths between points (e.g. shortest-path distance). We provide an extensive theoretical analysis of our algorithms, obtaining new results in structural graph theory as a byproduct. We also perform exhaustive empirical evaluation, including on-surface interpolation for rigid and deformable objects (in particular for mesh-dynamics modeling) as well as Wasserstein distance computations for point clouds, including the Gromov-Wasserstein variant.

Graph augmentation plays a crucial role in achieving good generalization for contrastive graph self-supervised learning. However, mainstream Graph Contrastive Learning (GCL) often favors random graph augmentations, by relying on random node dropout or edge perturbation on graphs. Random augmentations may inevitably lead to semantic information corruption during the training, and force the network to mistakenly focus on semantically irrelevant environmental background structures. To address these limitations and to improve generalization, we propose a novel self-supervised learning framework for GCL, which can adaptively screen the semantic-related substructure in graphs by capitalizing on the proposed gradient-based Graph Contrastive Saliency (GCS). The goal is to identify the most semantically discriminative structures of a graph via contrastive learning, such that we can generate semantically meaningful augmentations by leveraging on saliency. Empirical evidence on 16 benchmark datasets demonstrates the exclusive merits of the GCS-based framework. We also provide rigorous theoretical justification for GCS's robustness properties. Code is available at https://github.com/GCS2023/GCS .