NeurIPS 2024 论文列表

Message Passing Graph Neural Networks are known to suffer from two problems that are sometimes believed to be diametrically opposed: over-squashing and over-smoothing. The former results from topological bottlenecks that hamper the information flow from distant nodes and are mitigated by spectral gap maximization, primarily, by means of edge additions. However, such additions often promote over-smoothing that renders nodes of different classes less distinguishable. Inspired by the Braess phenomenon, we argue that deleting edges can address over-squashing and over-smoothing simultaneously. This insight explains how edge deletions can improve generalization, thus connecting spectral gap optimization to a seemingly disconnected objective of reducing computational resources by pruning graphs for lottery tickets. To this end, we propose a computationally effective spectral gap optimization framework to add or delete edges and demonstrate its effectiveness on the long range graph benchmark and on larger heterophilous datasets.

Graph Neural Networks (GNNs) have become essential in interpreting relational data across various domains, yet, they often struggle to generalize to unseen graph data that differs markedly from training instances. In this paper, we introduce a novel framework called General Retrieval-Augmented Graph Learning (RAGraph), which brings external graph data into the general graph foundation model to improve model generalization on unseen scenarios. On the top of our framework is a toy graph vector library that we established, which captures key attributes, such as features and task-specific label information. During inference, the RAGraph adeptly retrieves similar toy graphs based on key similarities in downstream tasks, integrating the retrieved data to enrich the learning context via the message-passing prompting mechanism. Our extensive experimental evaluations demonstrate that RAGraph significantly outperforms state-of-the-art graph learning methods in multiple tasks such as node classification, link prediction, and graph classification across both dynamic and static datasets. Furthermore, extensive testing confirms that RAGraph consistently maintains high performance without the need for task-specific fine-tuning, highlighting its adaptability, robustness, and broad applicability.

We present a new angle on the expressive power of graph neural networks (GNNs) by studying how the predictions of real-valued GNN classifiers, such as those classifying graphs probabilistically, evolve as we apply them on larger graphs drawn from some random graph model. We show that the output converges to a constant function, which upper-bounds what these classifiers can uniformly express. This strong convergence phenomenon applies to a very wide class of GNNs, including state of the art models, with aggregates including mean and the attention-based mechanism of graph transformers. Our results apply to a broad class of random graph models, including sparse and dense variants of the Erdős-Rényi model, the stochastic block model, and the Barabási-Albert model. We empirically validate these findings, observing that the convergence phenomenon appears not only on random graphs but also on some real-world graphs.

Spatial Message Passing Graph Neural Networks (MPGNNs) are widely used for learning on graph-structured data. However, key limitations of *ℓ*-step MPGNNs are that their "receptive field" is typically limited to the *ℓ*-hop neighborhood of a node and that information exchange between distant nodes is limited by over-squashing. Motivated by these limitations, we propose *Spatio-Spectral Graph Neural Networks (S²GNNs)* – a new modeling paradigm for Graph Neural Networks (GNNs) that synergistically combines spatially and spectrally parametrized graph filters. Parameterizing filters partially in the frequency domain enables global yet efficient information propagation. We show that S²GNNs vanquish over-squashing and yield strictly tighter approximation-theoretic error bounds than MPGNNs. Further, rethinking graph convolutions at a fundamental level unlocks new design spaces. For example, S²GNNs allow for free positional encodings that make them strictly more expressive than the 1-Weisfeiler-Leman (WL) test. Moreover, to obtain general-purpose S²GNNs, we propose spectrally parametrized filters for directed graphs. S²GNNs outperform spatial MPGNNs, graph transformers, and graph rewirings, e.g., on the peptide long-range benchmark tasks, and are competitive with state-of-the-art sequence modeling. On a 40 GB GPU, S²GNNs scale to millions of nodes.

Signed graphs can model friendly or antagonistic relations where edges are annotated with a positive or negative sign. The main downstream task in signed graph analysis is $\textit{link sign prediction}$. Signed Graph Neural Networks (SGNNs) have been widely used for signed graph representation learning. While significant progress has been made in SGNNs research, two issues (i.e., graph sparsity and unbalanced triangles) persist in the current SGNN models. We aim to alleviate these issues through data augmentation ($\textit{DA}$) techniques which have demonstrated effectiveness in improving the performance of graph neural networks. However, most graph augmentation methods are primarily aimed at graph-level and node-level tasks (e.g., graph classification and node classification) and cannot be directly applied to signed graphs due to the lack of side information (e.g., node features and label information) in available real-world signed graph datasets. Random $\textit{DropEdge} $is one of the few $\textit{DA}$ methods that can be directly used for signed graph data augmentation, but its effectiveness is still unknown. In this paper, we first provide the generalization bound for the SGNN model and demonstrate from both experimental and theoretical perspectives that the random $\textit{DropEdge}$ cannot improve the performance of link sign prediction. Therefore, we propose a novel signed graph augmentation method, $\underline{S}$igned $\underline{G}$raph $\underline{A}$ugmentation framework (SGA). Specifically, SGA first integrates a structure augmentation module to detect candidate edges solely based on network information. Furthermore, SGA incorporates a novel strategy to select beneficial candidates. Finally, SGA introduces a novel data augmentation perspective to enhance the training process of SGNNs. Experiment results on six real-world datasets demonstrate that SGA effectively boosts the performance of diverse SGNN models, achieving improvements of up to 32.3\% in F1-micro for SGCN on the Slashdot dataset in the link sign prediction task.

Traditional knowledge graph embedding (KGE) models map entities and relations to unique embedding vectors in a shallow lookup manner. As the scale of data becomes larger, this manner will raise unaffordable computational costs. Anchor-based strategies have been treated as effective ways to alleviate such efficiency problems by propagation on representative entities instead of the whole graph. However, most existing anchor-based KGE models select the anchors in a primitive manner, which limits their performance. To this end, we propose a novel anchor-based strategy for KGE, i.e., a relational clustering-based anchor selection strategy (RecPiece), where two characteristics are leveraged, i.e., (1) representative ability of the cluster centroids and (2) descriptive ability of relation types in KGs. Specifically, we first perform clustering over features of factual triplets instead of entities, where cluster number is naturally set as number of relation types since each fact can be characterized by its relation in KGs. Then, representative triplets are selected around the clustering centroids, further mapped into corresponding anchor entities. Extensive experiments on six datasets show that RecPiece achieves higher performances but comparable or even fewer parameters compared to previous anchor-based KGE models, indicating that our model can select better anchors in a more scalable way.

We investigate the entity alignment (EA) problem with unlabeled dangling cases, meaning that partial entities have no counterparts in the other knowledge graph (KG), yet these entities are unlabeled. The problem arises when the source and target graphs are of different scales, and it is much cheaper to label the matchable pairs than the dangling entities. To address this challenge, we propose the framework \textit{Lambda} for dangling detection and entity alignment. Lambda features a GNN-based encoder called KEESA with a spectral contrastive learning loss for EA and a positive-unlabeled learning algorithm called iPULE for dangling detection. Our dangling detection module offers theoretical guarantees of unbiasedness, uniform deviation bounds, and convergence. Experimental results demonstrate that each component contributes to overall performances that are superior to baselines, even when baselines additionally exploit 30\% of dangling entities labeled for training.

Graph Neural Networks (GNNs) have shown superior performance in node classification. However, GNNs perform poorly in the Few-Shot Node Classification (FSNC) task that requires robust generalization to make accurate predictions for unseen classes with limited labels. To tackle the challenge, we propose the integration of Sharpness-Aware Minimization (SAM)--a technique designed to enhance model generalization by finding a flat minimum of the loss landscape--into GNN training. The standard SAM approach, however, consists of two forward-backward steps in each training iteration, doubling the computational cost compared to the base optimizer (e.g., Adam). To mitigate this drawback, we introduce a novel algorithm, Fast Graph Sharpness-Aware Minimization (FGSAM), that integrates the rapid training of Multi-Layer Perceptrons (MLPs) with the superior performance of GNNs. Specifically, we utilize GNNs for parameter perturbation while employing MLPs to minimize the perturbed loss so that we can find a flat minimum with good generalization more efficiently. Moreover, our method reutilizes the gradient from the perturbation phase to incorporate graph topology into the minimization process at almost zero additional cost. To further enhance training efficiency, we develop FGSAM+ that executes exact perturbations periodically. Extensive experiments demonstrate that our proposed algorithm outperforms the standard SAM with lower computational costs in FSNC tasks. In particular, our FGSAM+ as a SAM variant offers a faster optimization than the base optimizer in most cases. In addition to FSNC, our proposed methods also demonstrate competitive performance in the standard node classification task for heterophilic graphs, highlighting the broad applicability.

Subgraph GNNs enhance message-passing GNNs expressivity by representing graphs as sets of subgraphs, demonstrating impressive performance across various tasks. However, their scalability is hindered by the need to process large numbers of subgraphs. While previous approaches attempted to generate smaller subsets of subgraphs through random or learnable sampling, these methods often yielded suboptimal selections or were limited to small subset sizes, ultimately compromising their effectiveness. This paper introduces a new Subgraph GNN framework to address these issues. Our approach diverges from most previous methods by associating subgraphs with node clusters rather than with individual nodes. We show that the resulting collection of subgraphs can be viewed as the product of coarsened and original graphs, unveiling a new connectivity structure on which we perform generalized message passing. Crucially, controlling the coarsening function enables meaningful selection of any number of subgraphs. In addition, we reveal novel permutation symmetries in the resulting node feature tensor, characterize associated linear equivariant layers, and integrate them into our Subgraph GNN. We also introduce novel node marking strategies and provide a theoretical analysis of their expressive power and other key aspects of our approach. Extensive experiments on multiple graph learning benchmarks demonstrate that our method is significantly more flexible than previous approaches, as it can seamlessly handle any number of subgraphs, while consistently outperforming baseline approaches. Our code is available at https://github.com/BarSGuy/Efficient-Subgraph-GNNs.

We introduce $r$-loopy Weisfeiler-Leman ($r$-$\ell$WL), a novel hierarchy of graph isomorphism tests and a corresponding GNN framework, $r$-$\ell$MPNN, that can count cycles up to length $r{+}2$. Most notably, we show that $r$-$\ell$WL can count homomorphisms of cactus graphs. This extends 1-WL, which can only count homomorphisms of trees and, in fact, is incomparable to $k$-WL for any fixed $k$. We empirically validate the expressive and counting power of $r$-$\ell$MPNN on several synthetic datasets and demonstrate the scalability and strong performance on various real-world datasets, particularly on sparse graphs.

Mastering games is a hard task, as games can be extremely complex, and still fundamentally different in structure from one another. While the AlphaZero algorithm has demonstrated an impressive ability to learn the rules and strategy of a large variety of games, ranging from Go and Chess, to Atari games, its reliance on extensive computational resources and rigid Convolutional Neural Network (CNN) architecture limits its adaptability and scalability. A model trained to play on a $19\times 19$ Go board cannot be used to play on a smaller $13\times 13$ board, despite the similarity between the two Go variants. In this paper, we focus on Chess, and explore using a more generic Graph-based Representation of a game state, rather than a grid-based one, to introduce a more general architecture based on Graph Neural Networks (GNN). We also expand the classical Graph Attention Network (GAT) layer to incorporate edge-features, to naturally provide a generic policy output format. Our experiments, performed on smaller networks than the initial AlphaZero paper, show that this new architecture outperforms previous architectures with a similar number of parameters, being able to increase playing strength an order of magnitude faster. We also show that the model, when trained on a smaller $5\times 5$ variant of chess, is able to be quickly fine-tuned to play on regular $8\times 8$ chess, suggesting that this approach yields promising generalization abilities. Our code is available at https://github.com/akulen/AlphaGateau.

We study how information propagates in decoder-only Transformers, which are the architectural foundation of most existing frontier large language models (LLMs). We rely on a theoretical signal propagation analysis---specifically, we analyse the representations of the last token in the final layer of the Transformer, as this is the representation used for next-token prediction. Our analysis reveals a representational collapse phenomenon: we prove that certain distinct pairs of inputs to the Transformer can yield arbitrarily close representations in the final token. This effect is exacerbated by the low-precision floating-point formats frequently used in modern LLMs. As a result, the model is provably unable to respond to these sequences in different ways---leading to errors in, e.g., tasks involving counting or copying. Further, we show that decoder-only Transformer language models can lose sensitivity to specific tokens in the input, which relates to the well-known phenomenon of over-squashing in graph neural networks. We provide empirical evidence supporting our claims on contemporary LLMs. Our theory points to simple solutions towards ameliorating these issues.

This paper pertains to an emerging machine learning paradigm: learning higher- order functions, i.e. functions whose inputs are functions themselves, particularly when these inputs are Neural Networks (NNs). With the growing interest in architectures that process NNs, a recurring design principle has permeated the field: adhering to the permutation symmetries arising from the connectionist structure of NNs. However, are these the sole symmetries present in NN parameterizations? Zooming into most practical activation functions (e.g. sine, ReLU, tanh) answers this question negatively and gives rise to intriguing new symmetries, which we collectively refer to as scaling symmetries, that is, non-zero scalar multiplications and divisions of weights and biases. In this work, we propose Scale Equivariant Graph MetaNetworks - ScaleGMNs, a framework that adapts the Graph Metanetwork (message-passing) paradigm by incorporating scaling symmetries and thus rendering neuron and edge representations equivariant to valid scalings. We introduce novel building blocks, of independent technical interest, that allow for equivariance or invariance with respect to individual scalar multipliers or their product and use them in all components of ScaleGMN. Furthermore, we prove that, under certain expressivity conditions, ScaleGMN can simulate the forward and backward pass of any input feedforward neural network. Experimental results demonstrate that our method advances the state-of-the-art performance for several datasets and activation functions, highlighting the power of scaling symmetries as an inductive bias for NN processing. The source code is publicly available at https://github.com/jkalogero/scalegmn.

Graph neural networks (GNNs) employing message passing for graph classification are inherently limited by the expressive power of the Weisfeiler-Leman (WL) test for graph isomorphism. Node individualization schemes, which assign unique identifiers to nodes (e.g., by adding random noise to features), are a common approach for achieving universal expressiveness. However, the ability of GNNs endowed with individualization schemes to generalize beyond the training data is still an open question. To address this question, this paper presents a theoretical analysis of the sample complexity of such GNNs from a statistical learning perspective, employing Vapnik–Chervonenkis (VC) dimension and covering number bounds. We demonstrate that node individualization schemes that are permutation-equivariant result in lower sample complexity, and design novel individualization schemes that exploit these results. As an application of this analysis, we also develop a novel architecture that can perform substructure identification (i.e., subgraph isomorphism) while having a lower VC dimension compared to competing methods. Finally, our theoretical findings are validated experimentally on both synthetic and real-world datasets.

Enhancing node-level Out-Of-Distribution (OOD) generalization on graphs remains a crucial area. In this paper, we develop a Structural Causal Model (SCM) to theoretically dissect the performance of two prominent invariant learning methods--Invariant Risk Minimization (IRM) and Variance-Risk Extrapolation (VREx)--in node-level OOD settings. Our analysis reveals a critical limitation: these methods may struggle to identify invariant features due to the complexities introduced by the message-passing mechanism, which can obscure causal features within a range of neighboring samples. To address this, we propose Cross-environment Intra-class Alignment (CIA), which explicitly eliminates spurious features by aligning representations within the same class, bypassing the need for explicit knowledge of underlying causal patterns. To adapt CIA to node-level OOD scenarios where environment labels are hard to obtain, we further propose CIA-LRA (Localized Reweighting Alignment) that leverages the distribution of neighboring labels to selectively align node representations, effectively distinguishing and preserving invariant features while removing spurious ones, all without relying on environment labels. We theoretically prove CIA-LRA's effectiveness by deriving an OOD generalization error bound based on PAC-Bayesian analysis. Experiments on graph OOD benchmarks validate the superiority of CIA and CIA-LRA, marking a significant advancement in node-level OOD generalization.

Graph self-supervised learning, as a powerful pre-training paradigm for Graph Neural Networks (GNNs) without labels, has received considerable attention. We have witnessed the success of graph self-supervised learning on pre-training the parameters of GNNs, leading many not to doubt that whether the learned GNNs parameters are all useful. In this paper, by presenting the experimental evidence and analysis, we surprisingly discover that the graph self-supervised learning models are highly redundant at both of neuron and layer levels, e.g., even randomly removing 51.6\% of parameters, the performance of graph self-supervised learning models still retains at least 96.2\%. This discovery implies that the parameters of graph self-supervised models can be largely reduced, making simultaneously fine-tuning both graph self-supervised learning models and prediction layers more feasible. Therefore, we further design a novel graph pre-training and fine-tuning paradigm called SLImming DE-correlation Fine-tuning (SLIDE). The effectiveness of SLIDE is verified through extensive experiments on various benchmarks, and the performance can be even improved with fewer parameters of models in most cases. For example, in comparison with full fine-tuning GraphMAE on Amazon-Computers dataset, even randomly reducing 40\% of parameters, we can still achieve the improvement of 0.24\% and 0.27\% for Micro-F1 and Macro-F1 scores respectively.