ICLR 2023 Papers

Although Transformer architectures have been successfully applied to graph data with the advent of Graph Transformer, current design of Graph Transformer still heavily relies on human labor and expertise knowledge to decide proper neural architectures and suitable graph encoding strategies at each Transformer layer. In literature, there have been some works on automated design of Transformers focusing on non-graph data such as texts and images without considering graph encoding strategies, which fail to handle the non-euclidean graph data. In this paper, we study the problem of automated graph Transformer, for the first time. However, solving these problems poses the following challenges: i) how can we design a unified search space for graph Transformer, and ii) how to deal with the coupling relations between Transformer architectures and the graph encodings of each Transformer layer. To address these challenges, we propose Automated Graph Transformer (AutoGT), a neural architecture search framework that can automatically discover the optimal graph Transformer architectures by joint optimization of Transformer architecture and graph encoding strategies. Specifically, we first propose a unified graph Transformer formulation that can represent most of state-of-the-art graph Transformer architectures. Based upon the unified formulation, we further design the graph Transformer search space that includes both candidate architectures and various graph encodings. To handle the coupling relations, we propose a novel encoding-aware performance estimation strategy by gradually training and splitting the supernets according to the correlations between graph encodings and architectures. The proposed strategy can provide a more consistent and fine-grained performance prediction when evaluating the jointly optimized graph encodings and architectures. Extensive experiments and ablation studies show that our proposed AutoGT gains sufficient improvement over state-of-the-art hand-crafted baselines on all datasets, demonstrating its effectiveness and wide applicability.

Inductive one-bit matrix completion is motivated by modern applications such as recommender systems, where new users would appear at test stage with the ratings consisting of only ones and no zeros. We propose a unified graph signal sampling framework which enjoys the benefits of graph signal analysis and processing. The key idea is to transform each user's ratings on the items to a function (signal) on the vertices of an item-item graph, then learn structural graph properties to recover the function from its values on certain vertices --- the problem of graph signal sampling. We propose a class of regularization functionals that takes into account discrete random label noise in the graph vertex domain, then develop the GS-IMC approach which biases the reconstruction towards functions that vary little between adjacent vertices for noise reduction. Theoretical result shows that accurate reconstructions can be achieved under mild conditions. For the online setting, we develop a Bayesian extension, i.e., BGS-IMC which considers continuous random Gaussian noise in the graph Fourier domain and builds upon a prediction-correction update algorithm to obtain the unbiased and minimum-variance reconstruction. Both GS-IMC and BGS-IMC have closed-form solutions and thus are highly scalable in large data. Experiments show that our methods achieve state-of-the-art performance on public benchmarks.

Graph neural network (GNN) is a powerful learning approach for graph-based recommender systems. Recently, GNNs integrated with contrastive learning have shown superior performance in recommendation with their data augmentation schemes, aiming at dealing with highly sparse data. Despite their success, most existing graph contrastive learning methods either perform stochastic augmentation (e.g., node/edge perturbation) on the user-item interaction graph, or rely on the heuristic-based augmentation techniques (e.g., user clustering) for generating contrastive views. We argue that these methods cannot well preserve the intrinsic semantic structures and are easily biased by the noise perturbation. In this paper, we propose a simple yet effective graph contrastive learning paradigm LightGCL that mitigates these issues impairing the generality and robustness of CL-based recommenders. Our model exclusively utilizes singular value decomposition for contrastive augmentation, which enables the unconstrained structural refinement with global collaborative relation modeling. Experiments conducted on several benchmark datasets demonstrate the significant improvement in performance of our model over the state-of-the-arts. Further analyses demonstrate the superiority of LightGCL's robustness against data sparsity and popularity bias. The source code of our model is available at https://github.com/HKUDS/LightGCL.

Graph Neural Networks (GNNs) have shown great promise in various graph learning tasks. However, the computational overheads of fitting GNNs to large-scale graphs grow rapidly, posing obstacles to GNNs from scaling up to real-world applications. To tackle this issue, Graph Lottery Ticket (GLT) hypothesis articulates that there always exists a sparse subnetwork/subgraph with admirable performance in GNNs with random initialization. Such a pair of core subgraph and sparse subnetwork (called graph lottery tickets) can be uncovered by iteratively applying a novel sparsification method. While GLT provides new insights for GNN compression, it requires a full pretraining process to obtain graph lottery tickets, which is not universal and friendly to real-world applications. Moreover, the graph sparsification in GLT utilizes sampling techniques, which may result in massive information loss and aggregation failure. In this paper, we explore the searching of graph lottery tickets from a complementary perspective -- transforming a random ticket into a graph lottery ticket, which allows us to more comprehensively explore the relationships between the original network/graph and their sparse counterpart. To achieve this, we propose regularization-based network pruning and hierarchical graph sparsification, leading to our Dual Graph Lottery Ticket (DGLT) framework for a joint sparsification of network and graph. Compared to GLT, our DGLT helps achieve a triple-win situation of graph lottery tickets with high sparsity, admirable performance, and good explainability. More importantly, we rigorously prove that our model can eliminate noise and maintain reliable information in substructures using the graph information bottleneck theory. Extensive experimental results on various graph-related tasks validate the effectiveness of our framework.

Oversmoothing is a central challenge of building more powerful Graph Neural Networks (GNNs). While previous works have only demonstrated that oversmoothing is inevitable when the number of graph convolutions tends to infinity, in this paper, we precisely characterize the mechanism behind the phenomenon via a non-asymptotic analysis. Specifically, we distinguish between two different effects when applying graph convolutions—an undesirable mixing effect that homogenizes node representations in different classes, and a desirable denoising effect that homogenizes node representations in the same class. By quantifying these two effects on random graphs sampled from the Contextual Stochastic Block Model (CSBM), we show that oversmoothing happens once the mixing effect starts to dominate the denoising effect, and the number of layers required for this transition is $O(\log N/\log (\log N))$ for sufficiently dense graphs with $N$ nodes. We also extend our analysis to study the effects of Personalized PageRank (PPR), or equivalently, the effects of initial residual connections on oversmoothing. Our results suggest that while PPR mitigates oversmoothing at deeper layers, PPR-based architectures still achieve their best performance at a shallow depth and are outperformed by the graph convolution approach on certain graphs. Finally, we support our theoretical results with numerical experiments, which further suggest that the oversmoothing phenomenon observed in practice can be magnified by the difficulty of optimizing deep GNN models.

Given a graph learning task, such as link prediction, on a new graph, how can we select the best method as well as its hyperparameters (collectively called a model) without having to train or evaluate any model on the new graph? Model selection for graph learning has been largely ad hoc. A typical approach has been to apply popular methods to new datasets, but this is often suboptimal. On the other hand, systematically comparing models on the new graph quickly becomes too costly, or even impractical. In this work, we develop the first meta-learning approach for evaluation-free graph learning model selection, called MetaGL, which utilizes the prior performances of existing methods on various benchmark graph datasets to automatically select an effective model for the new graph, without any model training or evaluations. To quantify similarities across a wide variety of graphs, we introduce specialized meta-graph features that capture the structural characteristics of a graph. Then we design G-M network, which represents the relations among graphs and models, and develop a graph-based meta-learner operating on this G-M network, which estimates the relevance of each model to different graphs. Extensive experiments show that using MetaGL to select a model for the new graph greatly outperforms several existing meta-learning techniques tailed for graph learning model selection (up to 47% better), while being extremely fast at test time (∼1 sec).

Tackling unfairness in graph learning models is a challenging task, as the unfairness issues on graphs involve both attributes and topological structures. Existing work on fair graph learning simply assumes that attributes of all nodes are available for model training and then makes fair predictions. In practice, however, the attributes of some nodes might not be accessible due to missing data or privacy concerns, which makes fair graph learning even more challenging. In this paper, we propose FairAC, a fair attribute completion method, to complement missing information and learn fair node embeddings for graphs with missing attributes. FairAC adopts an attention mechanism to deal with the attribute missing problem and meanwhile, it mitigates two types of unfairness, i.e., feature unfairness from attributes and topological unfairness due to attribute completion. FairAC can work on various types of homogeneous graphs and generate fair embeddings for them and thus can be applied to most downstream tasks to improve their fairness performance. To our best knowledge, FairAC is the first method that jointly addresses the graph attribution completion and graph unfairness problems. Experimental results on benchmark datasets show that our method achieves better fairness performance with less sacrifice in accuracy, compared with the state-of-the-art methods of fair graph learning. Code is available at: https://github.com/donglgcn/FairAC.

We consider representation learning for proteins with 3D structures. We build 3D graphs based on protein structures and develop graph networks to learn their representations. Depending on the levels of details that we wish to capture, protein representations can be computed at different levels, \emph{e.g.}, the amino acid, backbone, or all-atom levels. Importantly, there exist hierarchical relations among different levels. In this work, we propose to develop a novel hierarchical graph network, known as ProNet, to capture the relations. Our ProNet is very flexible and can be used to compute protein representations at different levels of granularity. By treating each amino acid as a node in graph modeling as well as harnessing the inherent hierarchies, our ProNet is more effective and efficient than existing methods. We also show that, given a base 3D graph network that is complete, our ProNet representations are also complete at all levels. Experimental results show that ProNet outperforms recent methods on most datasets. In addition, results indicate that different downstream tasks may require representations at different levels. Our code is publicly available as part of the DIG library (\url{https://github.com/divelab/DIG}).

Graph neural networks (GNNs) are prominent in the graph machine learning domain, owing to their strong performance across various tasks. A recent focal area is the space of graph self-supervised learning (SSL), which aims to derive useful node representations without labeled data. Notably, many state-of-the-art graph SSL methods are contrastive methods, which use a combination of positive and negative samples to learn node representations. Owing to challenges in negative sampling (slowness and model sensitivity), recent literature introduced non-contrastive methods, which instead only use positive samples. Though such methods have shown promising performance in node-level tasks, their suitability for link prediction tasks, which are concerned with predicting link existence between pairs of nodes (and have broad applicability to recommendation systems contexts) is yet unexplored. In this work, we extensively evaluate the performance of existing non-contrastive methods for link prediction in both transductive and inductive settings. While most existing non-contrastive methods perform poorly overall, we find that, surprisingly, BGRL generally performs well in transductive settings. However, it performs poorly in the more realistic inductive settings where the model has to generalize to links to/from unseen nodes. We find that non-contrastive models tend to overfit to the training graph and use this analysis to propose T-BGRL, a novel non-contrastive framework that incorporates cheap corruptions to improve the generalization ability of the model. This simple modification strongly improves inductive performance in 5/6 of our datasets, with up to a 120% improvement in Hits@50 - all with comparable speed to other non-contrastive baselines, and up to $14\times$ faster than the best-performing contrastive baseline. Our work imparts interesting findings about non-contrastive learning for link prediction and paves the way for future researchers to further expand upon this area.

Dynamic graphs are ubiquitous across disciplines where observations usually change over time. Regressions on dynamic graphs often contribute to diverse critical tasks, such as climate early-warning and traffic controlling. Existing homophily Graph Neural Networks (GNNs) adopt physical connections or feature similarity as adjacent matrix to perform node-level aggregations. However, on dynamic graphs with diverse node-wise relations, exploiting a pre-defined fixed topology for message passing inevitably leads to the aggregations of target-deviated neighbors. We designate such phenomenon as the topology-task discordance, which naturally challenges the homophily assumption. In this work, we revisit node-wise relationships and explore novel homophily measurements on dynamic graphs with both signs and distances, capturing multiple node-level spatial relations and temporal evolutions. We discover that advancing homophily aggregations to signed target-oriented message passing can effectively resolve the discordance and promote aggregation capacity. Therefore, a GReTo is proposed, which performs signed message passing in immediate neighborhood, and exploits both local environments and target awareness to realize high-order message propagation. Empirically, our solution achieves significant improvements against best baselines, notably improving 24.79% on KnowAir and 3.60% on Metr-LA.

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.

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.

Graph neural networks have been successfully adapted for learning vector representations of graphs through various neighborhood aggregation schemes. Previous researches suggest, however, that they possess limitations in incorporating key non-Euclidean topological properties of graphs. This paper mathematically identifies the caliber of graph neural networks in classifying isomorphism classes of graphs with continuous node attributes up to their local topological properties. In light of these observations, we construct the Cycle to Clique graph neural network, a novel yet simple algorithm which topologically enriches the input data of conventional graph neural networks while preserving their architectural components. This method theoretically outperforms conventional graph neural networks in classifying isomorphism classes of graphs while ensuring comparable time complexity in representing random graphs. Empirical results further support that the novel algorithm produces comparable or enhanced results in classifying benchmark graph data sets compared to contemporary variants of graph neural networks.

As graph data size increases, the vast latency and memory consumption during inference pose a significant challenge to the real-world deployment of Graph Neural Networks (GNNs). While quantization is a powerful approach to reducing GNNs complexity, most previous works on GNNs quantization fail to exploit the unique characteristics of GNNs, suffering from severe accuracy degradation. Through an in-depth analysis of the topology of GNNs, we observe that the topology of the graph leads to significant differences between nodes, and most of the nodes in a graph appear to have a small aggregation value. Motivated by this, in this paper, we propose the Aggregation-Aware mixed-precision Quantization ($\rm A^2Q$) for GNNs, where an appropriate bitwidth is automatically learned and assigned to each node in the graph. To mitigate the vanishing gradient problem caused by sparse connections between nodes, we propose a Local Gradient method to serve the quantization error of the node features as the supervision during training. We also develop a Nearest Neighbor Strategy to deal with the generalization on unseen graphs. Extensive experiments on eight public node-level and graph-level datasets demonstrate the generality and robustness of our proposed method. Compared to the FP32 models, our method can achieve up to $18.8\times$ (i.e., 1.70bits) compression ratio with negligible accuracy degradation. Moreover, compared to the state-of-the-art quantization method, our method can achieve up to $11.4\%$ and $9.5\%$ accuracy improvements on the node-level and graph-level tasks, respectively, and up to $2\times$ speedup on a dedicated hardware accelerator.

Point cloud data is ubiquitous in scientific fields. Recently, geometric deep learning (GDL) has been widely applied to solve prediction tasks with such data. However, GDL models are often complicated and hardly interpretable, which poses concerns to scientists who are to deploy these models in scientific analysis and experiments. This work proposes a general mechanism, learnable randomness injection (LRI), which allows building inherently interpretable models based on general GDL backbones. LRI-induced models, once trained, can detect the points in the point cloud data that carry information indicative of the prediction label. We also propose four datasets from real scientific applications that cover the domains of high-energy physics and biochemistry to evaluate the LRI mechanism. Compared with previous post-hoc interpretation methods, the points detected by LRI align much better and stabler with the ground-truth patterns that have actual scientific meanings. LRI is grounded by the information bottleneck principle, and thus LRI-induced models are also more robust to distribution shifts between training and test scenarios. Our code and datasets are available at https://github.com/Graph-COM/LRI.

Recently, graph-based planning algorithms have gained much attention to solve goal-conditioned reinforcement learning (RL) tasks: they provide a sequence of subgoals to reach the target-goal, and the agents learn to execute subgoal-conditioned policies. However, the sample-efficiency of such RL schemes still remains a challenge, particularly for long-horizon tasks. To address this issue, we present a simple yet effective self-imitation scheme which distills a subgoal-conditioned policy into the target-goal-conditioned policy. Our intuition here is that to reach a target-goal, an agent should pass through a subgoal, so target-goal- and subgoal- conditioned policies should be similar to each other. We also propose a novel scheme of stochastically skipping executed subgoals in a planned path, which further improves performance. Unlike prior methods that only utilize graph-based planning in an execution phase, our method transfers knowledge from a planner along with a graph into policy learning. We empirically show that our method can significantly boost the sample-efficiency of the existing goal-conditioned RL methods under various long-horizon control tasks.

Electron cryo-microscopy (cryo-EM) produces three-dimensional (3D) maps of the electrostatic potential of biological macromolecules, including proteins. At sufficient resolution, the cryo-EM maps, along with some knowledge about the imaged molecules, allow de novo atomic modelling. Typically, this is done through a laborious manual process. Recent advances in machine learning applications to protein structure prediction show potential for automating this process. Taking inspiration from these techniques, we have built ModelAngelo for automated model building of proteins in cryo-EM maps. ModelAngelo first uses a residual convolutional neural network (CNN) to initialize a graph representation with nodes assigned to individual amino acids of the proteins in the map and edges representing the protein chain. The graph is then refined with a graph neural network (GNN) that combines the cryo-EM data, the amino acid sequence data and prior knowledge about protein geometries. The GNN refines the geometry of the protein chain and classifies the amino acids for each of its nodes. The final graph is post-processed with a hidden Markov model (HMM) search to map each protein chain to entries in a user provided sequence file. Application to 28 test cases shows that ModelAngelo outperforms state-of-the-art and approximates manual building for cryo-EM maps with resolutions better than 3.5 A.

The expressive power of Graph Neural Networks (GNNs) is fundamental for understanding their capabilities and limitations, i.e., what graph properties can or cannot be learnt by a GNN. Since standard GNNs have been characterised to be upper-bounded by the Weisfeiler-Lehman (1-WL) algorithm, recent attempts concentrated on developing more expressive GNNs in terms of the $k$-WL hierarchy, a well-established framework for graph isormorphism tests. In this work we show that, contrary to the widely accepted view, the $k$-WL hierarchy is not well-suited for measuring expressive GNNs. This is due to limitations that are inherent to high-dimensional WL algorithms such as the lack of a natural interpretation and high computational costs, which makes it difficult to draw any firm conclusions about the expressive power of GNNs beyond 1-WL. Thus, we propose a novel hierarchy of graph isomorphism tests, namely Neighbourhood WL ($\mathscr{N}$-WL), and also establish a new theorem on the equivalence of expressivity between induced connected subgraphs and induced subgraphs within this hierarchy. Further, we design a GNN model upon $\mathscr{N}$-WL, Graph Neighbourhood Neural Network (G3N), and empirically verify its expressive power on synthetic and real-world benchmarks.

The message passing-based graph neural networks (GNNs) have achieved great success in many real-world applications. However, training GNNs on large-scale graphs suffers from the well-known neighbor explosion problem, i.e., the exponentially increasing dependencies of nodes with the number of message passing layers. Subgraph-wise sampling methods---a promising class of mini-batch training techniques---discard messages outside the mini-batches in backward passes to avoid the neighbor explosion problem at the expense of gradient estimation accuracy. This poses significant challenges to their convergence analysis and convergence speeds, which seriously limits their reliable real-world applications. To address this challenge, we propose a novel subgraph-wise sampling method with a convergence guarantee, namely Local Message Compensation (LMC). To the best of our knowledge, LMC is the {\it first} subgraph-wise sampling method with provable convergence. The key idea of LMC is to retrieve the discarded messages in backward passes based on a message passing formulation of backward passes. By efficient and effective compensations for the discarded messages in both forward and backward passes, LMC computes accurate mini-batch gradients and thus accelerates convergence. We further show that LMC converges to first-order stationary points of GNNs. Experiments on large-scale benchmark tasks demonstrate that LMC significantly outperforms state-of-the-art subgraph-wise sampling methods in terms of efficiency.