ICLR 2024 Papers

Recently, Input Mixup, which augments virtual samples by interpolating input features and corresponding labels, is one of the promising methods to alleviate the over-fitting problem on various domains including image classification and natural language processing because of its ability to generate a variety of virtual samples, and ease of usability and versatility. However, designing Input Mixup for the node classification is still challenging due to the irregularity issue that each node contains a different number of neighboring nodes for input and the alignment issue that how to align and interpolate two sets of neighboring nodes is not well-defined when two nodes are interpolated. To address the issues, this paper proposes a novel Mixup method, called iGraphMix, tailored to node classification. Our method generates virtual nodes and their edges by interpolating input features and labels, and attaching sampled neighboring nodes. The virtual graphs generated by iGraphMix serve as inputs for graph neural networks (GNNs) training, thereby facilitating its easy application to various GNNs and enabling effective combination with other augmentation methods. We mathematically prove that training GNNs with iGraphMix leads to better generalization performance compared to that without augmentation, and our experiments support the theoretical findings.

We introduce Clifford Group Equivariant Simplicial Message Passing Networks, a method for steerable $\mathrm{E}(n)$-equivariant message passing on simplicial complexes. Our method integrates the expressivity of Clifford group-equivariant layers with simplicial message passing, which is topologically more intricate than regular graph message passing. Clifford algebras include higher-order objects such as bivectors and trivectors, which express geometric features (e.g., areas, volumes) derived from vectors. Using this knowledge, we represent simplex features through geometric products of their vertices. To achieve efficient simplicial message passing, we share the parameters of the message network across different dimensions. Additionally, we restrict the final message to an aggregation of the incoming messages from different dimensions, leading to what we term *shared* simplicial message passing. Experimental results show that our method is able to outperform both equivariant and simplicial graph neural networks on a variety of geometric tasks.

Deep graph clustering has recently received significant attention due to its ability to enhance the representation learning capabilities of models in unsupervised scenarios. Nevertheless, deep clustering for temporal graphs, which could capture crucial dynamic interaction information, has not been fully explored. It means that in many clustering-oriented real-world scenarios, temporal graphs can only be processed as static graphs. This not only causes the loss of dynamic information but also triggers huge computational consumption. To solve the problem, we propose a general framework for deep Temporal Graph Clustering called TGC, which introduces deep clustering techniques to suit the interaction sequence-based batch-processing pattern of temporal graphs. In addition, we discuss differences between temporal graph clustering and static graph clustering from several levels. To verify the superiority of the proposed framework TGC, we conduct extensive experiments. The experimental results show that temporal graph clustering enables more flexibility in finding a balance between time and space requirements, and our framework can effectively improve the performance of existing temporal graph learning methods. The code is released: https://github.com/MGitHubL/Deep-Temporal-Graph-Clustering.

Graph transformer has been proven as an effective graph learning method for its adoption of attention mechanism that is capable of capturing expressive representations from complex topological and feature information of graphs. Graph transformer conventionally performs dense attention (or global attention) for every pair of nodes to learn node representation vectors, resulting in quadratic computational costs that are unaffordable for large-scale graph data. Therefore, mini-batch training for graph transformers is a promising direction, but limited samples in each mini-batch can not support effective dense attention to encode informative representations. Facing this bottleneck, (1) we start by assigning each node a token list that is sampled by personalized PageRank (PPR) and then apply standard multi-head self-attention only on this list to compute its node representations. This PPR tokenization method decouples model training from complex graph topological information and makes heavy feature engineering offline and independent, such that mini-batch training of graph transformers is possible by loading each node's token list in batches. We further prove this PPR tokenization is viable as a graph convolution network with a fixed polynomial filter and jumping knowledge. However, only using personalized PageRank may limit information carried by a token list, which could not support different graph inductive biases for model training. To this end, (2) we rewire graphs by introducing multiple types of virtual connections through structure- and content-based super nodes that enable PPR tokenization to encode local and global contexts, long-range interaction, and heterophilous information into each node's token list, and then formalize our $\underline{\textbf{V}}$irtual $\underline{\textbf{C}}$onnection $\underline{\textbf{R}}$anking based $\underline{\textbf{Graph}}$ Trans$\underline{\textbf{former}}$ (VCR-Graphormer). Overall, VCR-Graphormer needs $O(m+klogk)$ complexity for graph tokenization as compared to $O(n^{3})$ of previous works. The [code](https://github.com/DongqiFu/VCR-Graphormer) is provided.

Comprehending natural language instructions is a charming property for 3D indoor scene synthesis systems. Existing methods directly model object joint distributions and express object relations implicitly within a scene, thereby hindering the controllability of generation. We introduce InstructScene, a novel generative framework that integrates a semantic graph prior and a layout decoder to improve controllability and fidelity for 3D scene synthesis. The proposed semantic graph prior jointly learns scene appearances and layout distributions, exhibiting versatility across various downstream tasks in a zero-shot manner. To facilitate the benchmarking for text-driven 3D scene synthesis, we curate a high-quality dataset of scene-instruction pairs with large language and multimodal models. Extensive experimental results reveal that the proposed method surpasses existing state-of-the-art approaches by a large margin. Thorough ablation studies confirm the efficacy of crucial design components. Project page: https://chenguolin.github.io/projects/InstructScene.

While contrastive self-supervised learning has become the de-facto learning paradigm for graph neural networks, the pursuit of higher task accuracy requires a larger hidden dimensionality to learn informative and discriminative full-precision representations, raising concerns about computation, memory footprint, and energy consumption burden (largely overlooked) for real-world applications. This work explores a promising direction for graph contrastive learning (GCL) with spiking neural networks (SNNs), which leverage sparse and binary characteristics to learn more biologically plausible and compact representations. We propose SpikeGCL, a novel GCL framework to learn binarized 1-bit representations for graphs, making balanced trade-offs between efficiency and performance. We provide theoretical guarantees to demonstrate that SpikeGCL has comparable expressiveness with its full-precision counterparts. Experimental results demonstrate that, with nearly 32x representation storage compression, SpikeGCL is either comparable to or outperforms many fancy state-of-the-art supervised and self-supervised methods across several graph benchmarks.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. Code available at https://github.com/Karami-m/HiGen_main.

We propose a new self-explainable Graph Neural Network (GNN) model: GraphChef. GraphChef integrates decision trees into the GNN message passing framework. Given a dataset, GraphChef returns a set of rules (a recipe) that explains each class in the dataset unlike existing GNNs and explanation methods that reason on individual graphs. Thanks to the decision trees, GraphChef recipes are human understandable. We also present a new pruning method to produce small and easy to digest trees. Experiments demonstrate that GraphChef reaches comparable accuracy to not self-explainable GNNs and produced decision trees are indeed small. We further validate the correctness of the discovered recipes on datasets where explanation ground truth is available: Reddit-Binary, MUTAG, BA-2Motifs, BA-Shapes, Tree-Cycle, and Tree-Grid.

Graph classification, which aims to predict a label for a graph, has many real-world applications such as malware detection, fraud detection, and healthcare. However, many studies show an attacker could carefully perturb the structure and/or node features in a graph such that a graph classifier misclassifies the perturbed graph. Such vulnerability impedes the deployment of graph classification in security/safety-critical applications. Existing empirical defenses lack formal robustness guarantees and could be broken by adaptive or unknown attacks. Existing provable defenses have the following limitations: 1) they achieve sub-optimal robustness guarantees for graph structure perturbation, 2) they cannot provide robustness guarantees for arbitrarily node feature perturbations, 3) their robustness guarantees are probabilistic, meaning they could be incorrect with a non-zero probability, and 4) they incur large computation costs. We aim to address those limitations in this work. We propose GNNCert, a certified defense against both graph structure and node feature perturbations for graph classification. Our GNNCert provably predicts the same label for a graph when the number of perturbed edges and the number of nodes with perturbed features are bounded. Our results on 8 benchmark datasets show that GNNCert outperforms three state-of-the-art methods.

Graph Neural Networks (GNNs) are widely deployed in vast fields, but they often struggle to maintain accurate representations as graphs evolve. We theoretically establish a lower bound, proving that under mild conditions, representation distortion inevitably occurs over time. To estimate the temporal distortion without human annotation after deployment, one naive approach is to pre-train a recurrent model (e.g., RNN) before deployment and use this model afterwards, but the estimation is far from satisfactory. In this paper, we analyze the representation distortion from an information theory perspective, and attribute it primarily to inaccurate feature extraction during evolution. Consequently, we introduce Smart, a straightforward and effective baseline enhanced by an adaptive feature extractor through self-supervised graph reconstruction. In synthetic random graphs, we further refine the former lower bound to show the inevitable distortion over time and empirically observe that Smart achieves good estimation performance. Moreover, we observe that Smart consistently shows outstanding generalization estimation on four real-world evolving graphs. The ablation studies underscore the necessity of graph reconstruction. For example, on OGB-arXiv dataset, the estimation metric MAPE deteriorates from 2.19% to 8.00% without reconstruction.

Equivariance is an important structural property that is captured by architectures such as graph neural networks (GNNs). However, equivariant graph functions cannot produce different outputs for similar nodes, which may be undesirable when the function is trying to optimize some global graph property. In this paper, we define orbit-equivariance, a relaxation of equivariance which allows for such functions whilst retaining important structural inductive biases. We situate the property in the hierarchy of graph functions, define a taxonomy of orbit-equivariant functions, and provide four different ways to achieve non-equivariant GNNs. For each, we analyze their expressivity with respect to orbit-equivariance and evaluate them on two novel datasets, one of which stems from a real-world use-case of designing optimal bioisosteres.

This paper focuses on graph metric learning. First, we present a class of maximum mean discrepancy (MMD) based graph kernels, called MMD-GK. These kernels are computed by applying MMD to the node representations of two graphs with message-passing propagation. Secondly, we provide a class of deep MMD-GKs that are able to learn graph kernels and implicit graph features adaptively in an unsupervised manner. Thirdly, we propose a class of supervised deep MMD-GKs that are able to utilize label information of graphs and hence yield more discriminative metrics. Besides the algorithms, we provide theoretical analysis for the proposed methods. The proposed methods are evaluated in comparison to many baselines such as graph kernels and graph neural networks in the tasks of graph clustering and graph classification. The numerical results demonstrate the effectiveness and superiority of our methods.

Structural and Positional Encodings can significantly improve the performance of Graph Neural Networks in downstream tasks. Recent literature has begun to systematically investigate differences in the structural properties that these approaches encode, as well as performance trade-offs between them. However, the question of which structural properties yield the most effective encoding remains open. In this paper, we investigate this question from a geometric perspective. We propose a novel structural encoding based on discrete Ricci curvature (Local Curvature Profiles, short LCP) and show that it significantly outperforms existing encoding approaches. We further show that combining local structural encodings, such as LCP, with global positional encodings improves downstream performance, suggesting that they capture complementary geometric information. Finally, we compare different encoding types with (curvature-based) rewiring techniques. Rewiring has recently received a surge of interest due to its ability to improve the performance of Graph Neural Networks by mitigating over-smoothing and over-squashing effects. Our results suggest that utilizing curvature information for structural encodings delivers significantly larger performance increases than rewiring.

The ground-state conformation of a molecule is often decisive for its properties. However, experimental or computational methods, such as density functional theory (DFT), are time-consuming and labor-intensive for obtaining this conformation. Deep learning (DL) based molecular representation learning (MRL) has made significant advancements in molecular modeling and has achieved remarkable results in various tasks. Consequently, it has emerged as a promising approach for directly predicting the ground-state conformation of molecules. In this regard, we introduce GTMGC, a novel network based on Graph-Transformer (GT) that seamlessly predicts the spatial configuration of molecules in a 3D space from their 2D topological architecture in an end-to-end manner. Moreover, we propose a novel self-attention mechanism called Molecule Structural Residual Self-Attention (MSRSA) for molecular structure modeling. This mechanism not only guarantees high model performance and easy implementation but also lends itself well to other molecular modeling tasks. Our method has been evaluated on the Molecule3D benchmark dataset and the QM9 dataset. Experimental results demonstrate that our approach achieves remarkable performance and outperforms current state-of-the-art methods as well as the widely used open-source software RDkit.

Many real-world networks evolve over time, and predicting the evolution of such networks remains a challenging task. Graph Neural Networks (GNNs) have shown empirical success for learning on static graphs, but they lack the ability to effectively learn from nodes and edges with different timestamps. Consequently, the prediction of future properties in temporal graphs remains a relatively under-explored area. In this paper, we aim to bridge this gap by introducing a principled framework, named GraphPulse. The framework combines two important techniques for the analysis of temporal graphs within a Newtonian framework. First, we employ the Mapper method, a key tool in topological data analysis, to extract essential clustering information from graph nodes. Next, we harness the sequential modeling capabilities of Recurrent Neural Networks (RNNs) for temporal reasoning regarding the graph's evolution. Through extensive experimentation, we demonstrate that our model enhances the ROC-AUC metric by 10.2\% in comparison to the top-performing state-of-the-art method across various temporal networks. We provide the implementation of GraphPulse at https://github.com/kiarashamsi/GraphPulse.

Equivariant message passing neural networks have emerged as the prevailing approach for predicting chemical properties of molecules due to their ability to leverage translation and rotation symmetries, resulting in a strong inductive bias. However, the equivariant operations in each layer can impose excessive constraints on the function form and network flexibility. To address these challenges, we introduce a novel network called the Hybrid Directional Graph Neural Network (HDGNN), which effectively combines strictly equivariant operations with learnable modules. We evaluate the performance of HDGNN on the QM9 dataset and the IS2RE dataset of OC20, demonstrating its state-of-the-art performance on several tasks and competitive performance on others. Our code is anonymously released on https://github.com/ajy112/HDGNN.

Graph Transformers (GTs) such as SAN and GPS are graph processing models that combine Message-Passing GNNs (MPGNNs) with global Self-Attention. They were shown to be universal function approximators, with two reservations: 1. The initial node features must be augmented with certain positional encodings. 2. The approximation is non-uniform: Graphs of different sizes may require a different approximating network. We first clarify that this form of universality is not unique to GTs: Using the same positional encodings, also pure MPGNNs and even 2-layer MLPs are non-uniform universal approximators. We then consider uniform expressivity: The target function is to be approximated by a single network for graphs of all sizes. There, we compare GTs to the more efficient MPGNN + Virtual Node architecture. The essential difference between the two model definitions is in their global computation method: Self-Attention Vs Virtual Node. We prove that none of the models is a uniform-universal approximator, before proving our main result: Neither model’s uniform expressivity subsumes the other’s. We demonstrate the theory with experiments on synthetic data. We further augment our study with real-world datasets, observing mixed results which indicate no clear ranking in practice as well.

Graph neural networks (GNNs) have achieved remarkable success across a wide range of applications, such as recommendation, drug discovery, and question answering. Behind the success of GNNs lies the backpropagation (BP) algorithm, which is the de facto standard for training deep neural networks (NNs). However, despite its effectiveness, BP imposes several constraints, which are not only biologically implausible, but also limit the scalability, parallelism, and flexibility in learning NNs. Examples of such constraints include storage of neural activities computed in the forward pass for use in the subsequent backward pass, and the dependence of parameter updates on non-local signals. To address these limitations, the forward-forward algorithm (FF) was recently proposed as an alternative to BP in the image classification domain, which trains NNs by performing two forward passes over positive and negative data. Inspired by this advance, we propose ForwardGNN in this work, a new forward learning procedure for GNNs, which avoids the constraints imposed by BP via an effective layer-wise local forward training. ForwardGNN extends the original FF to deal with graph data and GNNs, and makes it possible to operate without generating negative inputs (hence no longer forward-forward). Further, ForwardGNN enables each layer to learn from both the bottom-up and top-down signals without relying on the backpropagation of errors. Extensive experiments on real-world datasets show the effectiveness and generality of the proposed forward graph learning framework. We release our code at https://github.com/facebookresearch/forwardgnn.

Hyperspectral imaging (HSI) technology captures spectral information across a broad wavelength range, providing richer pixel features compared to traditional color images with only three channels. Although pixel classification in HSI has been extensively studied, especially using graph convolution neural networks (GCNs), quantifying epistemic and aleatoric uncertainties associated with the HSI classification (HSIC) results remains an unexplored area. These two uncertainties are effective for out-of-distribution (OOD) and misclassification detection, respectively. In this paper, we adapt two advanced uncertainty quantification models, evidential GCNs (EGCN) and graph posterior networks (GPN), designed for node classifications in graphs, into the realm of HSIC. We first reveal theoretically that a popular uncertainty cross-entropy (UCE) loss function is insufficient to produce good epistemic uncertainty when learning EGCNs. To mitigate the limitations, we propose two regularization terms. One leverages the inherent property of HSI data where each feature vector is a linear combination of the spectra signatures of the confounding materials, while the other is the total variation (TV) regularization to enforce the spatial smoothness of the evidence with edge-preserving. We demonstrate the effectiveness of the proposed regularization terms on both EGCN and GPN on three real-world HSIC datasets for OOD and misclassification detection tasks. The code is available at GitHub.