NeurIPS 2024 Papers

Equivariant machine learning is an approach for designing deep learning models that respect the symmetries of the problem, with the aim of reducing model complexity and improving generalization. In this paper, we focus on an extension of shift equivariance, which is the basis of convolution networks on images, to general graphs. Unlike images, graphs do not have a natural notion of domain translation. Therefore, we consider the graph functional shifts as the symmetry group: the unitary operators that commute with the graph shift operator. Notably, such symmetries operate in the signal space rather than directly in the spatial space. We remark that each linear filter layer of a standard spectral graph neural network (GNN) commutes with graph functional shifts, but the activation function breaks this symmetry. Instead, we propose nonlinear spectral filters (NLSFs) that are fully equivariant to graph functional shifts and show that they have universal approximation properties. The proposed NLSFs are based on a new form of spectral domain that is transferable between graphs. We demonstrate the superior performance of NLSFs over existing spectral GNNs in node and graph classification benchmarks.

Graph Transformers (GTs) have recently emerged as popular alternatives to traditional message-passing Graph Neural Networks (GNNs), due to their theoretically superior expressiveness and impressive performance reported on standard node classification benchmarks, often significantly outperforming GNNs. In this paper, we conduct a thorough empirical analysis to reevaluate the performance of three classic GNN models (GCN, GAT, and GraphSAGE) against GTs. Our findings suggest that the previously reported superiority of GTs may have been overstated due to suboptimal hyperparameter configurations in GNNs. Remarkably, with slight hyperparameter tuning, these classic GNN models achieve state-of-the-art performance, matching or even exceeding that of recent GTs across 17 out of the 18 diverse datasets examined. Additionally, we conduct detailed ablation studies to investigate the influence of various GNN configurations—such as normalization, dropout, residual connections, and network depth—on node classification performance. Our study aims to promote a higher standard of empirical rigor in the field of graph machine learning, encouraging more accurate comparisons and evaluations of model capabilities. Our implementation is available at https://github.com/LUOyk1999/tunedGNN.

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional `Pre-train \& Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates **SIX** pre-training methods and **FIVE** state-of-the-art graph prompt techniques, evaluated across **FIFTEEN** diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

Given the damping factor $\alpha$ and precision tolerance $\epsilon$, \citet{andersen2006local} introduced Approximate Personalized PageRank (APPR), the \textit{de facto local method} for approximating the PPR vector, with runtime bounded by $\Theta(1/(\alpha\epsilon))$ independent of the graph size. Recently, Fountoulakis \& Yang asked whether faster local algorithms could be developed using $\tilde{\mathcal{O}}(1/(\sqrt{\alpha}\epsilon))$ operations. By noticing that APPR is a local variant of Gauss-Seidel, this paper explores the question of *whether standard iterative solvers can be effectively localized*. We propose to use the *locally evolving set process*, a novel framework to characterize the algorithm locality, and demonstrate that many standard solvers can be effectively localized. Let $\overline{\operatorname{vol}}{ (\mathcal S_t)}$ and $\overline{\gamma_t}$ be the running average of volume and the residual ratio of active nodes $\textstyle \mathcal{S_t}$ during the process. We show $\overline{\operatorname{vol}}{ (\mathcal S_t)}/\overline{\gamma_t} \leq 1/\epsilon$ and prove APPR admits a new runtime bound $\tilde{\mathcal{O}}(\overline{\operatorname{vol}}(\mathcal S_t)/(\alpha\overline{\gamma_t}))$ mirroring the actual performance. Furthermore, when the geometric mean of residual reduction is $\Theta(\sqrt{\alpha})$, then there exists $c \in (0,2)$ such that the local Chebyshev method has runtime $\tilde{\mathcal{O}}(\overline{\operatorname{vol}}(\mathcal{S_t})/(\sqrt{\alpha}(2-c)))$ without the monotonicity assumption. Numerical results confirm the efficiency of this novel framework and show up to a hundredfold speedup over corresponding standard solvers on real-world graphs.

Graph retrieval based on subgraph isomorphism has several real-world applications such as scene graph retrieval, molecular fingerprint detection and circuit design. Roy et al. [35] proposed IsoNet, a late interaction model for subgraph matching, which first computes the node and edge embeddings of each graph independently of paired graph and then computes a trainable alignment map. Here, we present $\texttt{IsoNet++}$, an early interaction graph neural network (GNN), based on several technical innovations. First, we compute embeddings of all nodes by passing messages within and across the two input graphs, guided by an *injective alignment* between their nodes. Second, we update this alignment in a lazy fashion over multiple *rounds*. Within each round, we run a layerwise GNN from scratch, based on the current state of the alignment. After the completion of one round of GNN, we use the last-layer embeddings to update the alignments, and proceed to the next round. Third, $\texttt{IsoNet++}$ incorporates a novel notion of node-pair partner interaction. Traditional early interaction computes attention between a node and its potential partners in the other graph, the attention then controlling messages passed across graphs. We consider *node pairs* (not single nodes) as potential partners. Existence of an edge between the nodes in one graph and non-existence in the other provide vital signals for refining the alignment. Our experiments on several datasets show that the alignments get progressively refined with successive rounds, resulting in significantly better retrieval performance than existing methods. We demonstrate that all three innovations contribute to the enhanced accuracy. Our code and datasets are publicly available at https://github.com/structlearning/isonetpp.

While tokenized graph Transformers have demonstrated strong performance in node classification tasks, their reliance on a limited subset of nodes with high similarity scores for constructing token sequences overlooks valuable information from other nodes, hindering their ability to fully harness graph information for learning optimal node representations. To address this limitation, we propose a novel graph Transformer called GCFormer. Unlike previous approaches, GCFormer develops a hybrid token generator to create two types of token sequences, positive and negative, to capture diverse graph information. And a tailored Transformer-based backbone is adopted to learn meaningful node representations from these generated token sequences. Additionally, GCFormer introduces contrastive learning to extract valuable information from both positive and negative token sequences, enhancing the quality of learned node representations. Extensive experimental results across various datasets, including homophily and heterophily graphs, demonstrate the superiority of GCFormer in node classification, when compared to representative graph neural networks (GNNs) and graph Transformers.

Graph class incremental learning (GCIL) requires the model to classify emerging nodes of new classes while remembering old classes. Existing methods are designed to preserve effective information of old models or graph data to alleviate forgetting, but there is no clear theoretical understanding of what matters in information preservation. In this paper, we consider that present practice suffers from high semantic and structural shifts assessed by two devised shift metrics. We provide insights into information preservation in GCIL and find that maintaining graph information can preserve information of old models in theory to calibrate node semantic and graph structure shifts. We correspond graph information into low-frequency local-global information and high-frequency information in spatial domain. Based on the analysis, we propose a framework, Graph Spatial Information Preservation (GSIP). Specifically, for low-frequency information preservation, the old node representations obtained by inputting replayed nodes into the old model are aligned with the outputs of the node and its neighbors in the new model, and then old and new outputs are globally matched after pooling. For high-frequency information preservation, the new node representations are encouraged to imitate the near-neighbor pair similarity of old node representations. GSIP achieves a 10\% increase in terms of the forgetting metric compared to prior methods on large-scale datasets. Our framework can also seamlessly integrate existing replay designs. The code is available through https://github.com/Jillian555/GSIP.

We consider contextual bandits with graph feedback, a class of interactive learning problems with richer structures than vanilla contextual bandits, where taking an action reveals the rewards for all neighboring actions in the feedback graph under all contexts. Unlike the multi-armed bandits setting where a growing literature has painted a near-complete understanding of graph feedback, much remains unexplored in the contextual bandits counterpart. In this paper, we make inroads into this inquiry by establishing a regret lower bound $\Omega(\sqrt{\beta_M(G) T})$, where $M$ is the number of contexts, $G$ is the feedback graph, and $\beta_M(G)$ is our proposed graph-theoretic quantity that characterizes the fundamental learning limit for this class of problems. Interestingly, $\beta_M(G)$ interpolates between $\alpha(G)$ (the independence number of the graph) and $\mathsf{m}(G)$ (the maximum acyclic subgraph (MAS) number of the graph) as the number of contexts $M$ varies. We also provide algorithms that achieve near-optimal regret for important classes of context sequences and/or feedback graphs, such as transitively closed graphs that find applications in auctions and inventory control. In particular, with many contexts, our results show that the MAS number essentially characterizes the statistical complexity for contextual bandits, as opposed to the independence number in multi-armed bandits.

Graph coarsening aims to reduce the size of a large graph while preserving some of its key properties, which has been used in many applications to reduce computational load and memory footprint. For instance, in graph machine learning, training Graph Neural Networks (GNNs) on coarsened graphs leads to drastic savings in time and memory. However, GNNs rely on the Message-Passing (MP) paradigm, and classical spectral preservation guarantees for graph coarsening do not directly lead to theoretical guarantees when performing naive message-passing on the coarsened graph. In this work, we propose a new message-passing operation specific to coarsened graphs, which exhibit theoretical guarantees on the preservation of the propagated signal. Interestingly, and in a sharp departure from previous proposals, this operation on coarsened graphs is oriented, even when the original graph is undirected. We conduct node classification tasks on synthetic and real data and observe improved results compared to performing naive message-passing on the coarsened graph.

Analyzing the motion of multiple biological agents, be it cells or individual animals, is pivotal for the understanding of complex collective behaviors. With the advent of advanced microscopy, detailed images of complex tissue formations involving multiple cell types have become more accessible in recent years. However, deciphering the underlying rules that govern cell movements is far from trivial. Here, we present a novel deep learning framework for estimating the underlying equations of motion from observed trajectories, a pivotal step in decoding such complex dynamics. Our framework integrates graph neural networks with neural differential equations, enabling effective prediction of two-body interactions based on the states of the interacting entities. We demonstrate the efficacy of our approach through two numerical experiments. First, we used simulated data from a toy model to tune the hyperparameters. Based on the obtained hyperparameters, we then applied this approach to a more complex model with non-reciprocal forces that mimic the collective dynamics of the cells of slime molds. Our results show that the proposed method can accurately estimate the functional forms of two-body interactions -- even when they are nonreciprocal -- thereby precisely replicating both individual and collective behaviors within these systems.

Despite the widespread adoption of Graph Neural Networks (GNNs), these models often incorporate off-the-shelf normalization layers like BatchNorm or InstanceNorm, which were not originally designed for GNNs. Consequently, these normalization layers may not effectively capture the unique characteristics of graph-structured data, potentially even weakening the expressive power of the overall architecture. While existing graph-specific normalization layers have been proposed, they often struggle to offer substantial and consistent benefits. In this paper, we propose GRANOLA, a novel graph-adaptive normalization layer. Unlike existing normalization layers, GRANOLA normalizes node features by adapting to the specific characteristics of the graph, particularly by generating expressive representations of its nodes, obtained by leveraging the propagation of Random Node Features (RNF) in the graph. We provide theoretical results that support our design choices as well as an extensive empirical evaluation demonstrating the superior performance of GRANOLA over existing normalization techniques. Furthermore, GRANOLA emerges as the top-performing method among all baselines in the same time complexity class of Message Passing Neural Networks (MPNNs).

Power grids are critical infrastructures of paramount importance to modern society and, therefore, engineered to operate under diverse conditions and failures. The ongoing energy transition poses new challenges for the decision-makers and system operators. Therefore, we must develop grid analysis algorithms to ensure reliable operations. These key tools include power flow analysis and system security analysis, both needed for effective operational and strategic planning. The literature review shows a growing trend of machine learning (ML) models that perform these analyses effectively. In particular, Graph Neural Networks (GNNs) stand out in such applications because of the graph-based structure of power grids. However, there is a lack of publicly available graph datasets for training and benchmarking ML models in electrical power grid applications. First, we present PowerGraph, which comprises GNN-tailored datasets for i) power flows, ii) optimal power flows, and iii) cascading failure analyses of power grids. Second, we provide ground-truth explanations for the cascading failure analysis. Finally, we perform a complete benchmarking of GNN methods for node-level and graph-level tasks and explainability. Overall, PowerGraph is a multifaceted GNN dataset for diverse tasks that includes power flow and fault scenarios with real-world explanations, providing a valuable resource for developing improved GNN models for node-level, graph-level tasks and explainability methods in power system modeling. The dataset is available at https://figshare.com/articles/dataset/PowerGraph/22820534 and the code at https://github.com/PowerGraph-Datasets.

Graph Neural Networks (GNNs) have demonstrated remarkable performance across a spectrum of graph-related tasks, however concerns persist regarding their vulnerability to adversarial perturbations. While prevailing defense strategies focus primarily on pre-processing techniques and adaptive message-passing schemes, this study delves into an under-explored dimension: the impact of weight initialization and associated hyper-parameters, such as training epochs, on a model’s robustness. We introduce a theoretical framework bridging the connection between initialization strategies and a network's resilience to adversarial perturbations. Our analysis reveals a direct relationship between initial weights, number of training epochs and the model’s vulnerability, offering new insights into adversarial robustness beyond conventional defense mechanisms. While our primary focus is on GNNs, we extend our theoretical framework, providing a general upper-bound applicable to Deep Neural Networks. Extensive experiments, spanning diverse models and real-world datasets subjected to various adversarial attacks, validate our findings. We illustrate that selecting appropriate initialization not only ensures performance on clean datasets but also enhances model robustness against adversarial perturbations, with observed gaps of up to 50\% compared to alternative initialization approaches.

Graph neural networks (GNNs) have emerged as powerful tools for processing relational data in applications. However, GNNs suffer from the problem of oversmoothing, the property that features of all nodes exponentially converge to the same vector over layers, prohibiting the design of deep GNNs. In this work we study oversmoothing in graph convolutional networks (GCNs) by using their Gaussian process (GP) equivalence in the limit of infinitely many hidden features. By generalizing methods from conventional deep neural networks (DNNs), we can describe the distribution of features at the output layer of deep GCNs in terms of a GP: as expected, we find that typical parameter choices from the literature lead to oversmoothing. The theory, however, allows us to identify a new, non-oversmoothing phase: if the initial weights of the network have sufficiently large variance, GCNs do not oversmooth, and node features remain informative even at large depth. We demonstrate the validity of this prediction in finite-size GCNs by training a linear classifier on their output. Moreover, using the linearization of the GCN GP, we generalize the concept of propagation depth of information from DNNs to GCNs. This propagation depth diverges at the transition between the oversmoothing and non-oversmoothing phase. We test the predictions of our approach and find good agreement with finite-size GCNs. Initializing GCNs near the transition to the non-oversmoothing phase, we obtain networks which are both deep and expressive.

In the era of big data, graphs have emerged as a natural representation of intricate relationships. However, graph sizes often become unwieldy, leading to storage, computation, and analysis challenges. A crucial demand arises for methods that can effectively downsize large graphs while retaining vital insights. Graph coarsening seeks to simplify large graphs while maintaining the basic statistics of the graphs, such as spectral properties and $\epsilon$-similarity in the coarsened graph. This ensures that downstream processes are more efficient and effective. Most published methods are suitable for homophilic datasets, limiting their universal use. We propose **U**niversal **G**raph **C**oarsening (UGC), a framework equally suitable for homophilic and heterophilic datasets. UGC integrates node attributes and adjacency information, leveraging the dataset's heterophily factor. Results on benchmark datasets demonstrate that UGC preserves spectral similarity while coarsening. In comparison to existing methods, UGC is 4x to 15x faster, has lower eigen-error, and yields superior performance on downstream processing tasks even at 70% coarsening ratios.

In this paper, we introduce the first learning-free model reuse task within the non-Euclidean domain, termed as Deep Graph Mating (Grama). We strive to create a child Graph Neural Network (GNN) that integrates knowledge from pre-trained parent models without requiring re-training, fine-tuning, or annotated labels. To this end, we begin by investigating the permutation invariance property of GNNs, which leads us to develop two vanilla approaches for Grama: Vanilla Parameter Interpolation (VPI) and Vanilla Alignment Prior to Interpolation (VAPI), both employing topology-independent interpolation in the parameter space. However, neither approach has achieved the anticipated results. Through theoretical analysis of VPI and VAPI, we identify critical challenges unique to Grama, including increased sensitivity to parameter misalignment and further the inherent topology-dependent complexities. Motivated by these findings, we propose the Dual-Message Coordination and Calibration (DuMCC) methodology, comprising the Parent Message Coordination (PMC) scheme to optimise the permutation matrices for parameter interpolation by coordinating aggregated messages, and the Child Message Calibration (CMC) scheme to mitigate over-smoothing identified in PMC by calibrating the message statistics within child GNNs. Experiments across diverse domains, including node and graph property prediction, 3D object recognition, and large-scale semantic parsing, demonstrate that the proposed DuMCC effectively enables training-free knowledge transfer, yielding results on par with those of pre-trained models.

We introduce the Distributed-order fRActional Graph Operating Network (DRAGON), a novel continuous Graph Neural Network (GNN) framework that incorporates distributed-order fractional calculus. Unlike traditional continuous GNNs that utilize integer-order or single fractional-order differential equations, DRAGON uses a learnable probability distribution over a range of real numbers for the derivative orders. By allowing a flexible and learnable superposition of multiple derivative orders, our framework captures complex graph feature updating dynamics beyond the reach of conventional models. We provide a comprehensive interpretation of our framework's capability to capture intricate dynamics through the lens of a non-Markovian graph random walk with node feature updating driven by an anomalous diffusion process over the graph. Furthermore, to highlight the versatility of the DRAGON framework, we conduct empirical evaluations across a range of graph learning tasks. The results consistently demonstrate superior performance when compared to traditional continuous GNN models. The implementation code is available at \url{https://github.com/zknus/NeurIPS-2024-DRAGON}.

In real-world scenarios, networks (graphs) and their tasks possess unique characteristics, requiring the development of a versatile graph augmentation (GA) to meet the varied demands of network analysis. Unfortunately, most Graph Contrastive Learning (GCL) frameworks are hampered by the specificity, complexity, and incompleteness of their GA techniques. Firstly, GAs designed for specific scenarios may compromise the universality of models if mishandled. Secondly, the process of identifying and generating optimal augmentations generally involves substantial computational overhead. Thirdly, the effectiveness of the GCL, even the learnable ones, is constrained by the finite selection of GAs available. To overcome the above limitations, this paper introduces a novel unified GA module dubbed UGA after reinterpreting the mechanism of GAs in GCLs from a message-passing perspective. Theoretically, this module is capable of unifying any explicit GAs, including node, edge, attribute, and subgraph augmentations. Based on the proposed UGA, a novel generalized GCL framework dubbed Graph cOntrastive UnifieD Augmentations (GOUDA) is proposed. It seamlessly integrates widely adopted contrastive losses and an introduced independence loss to fulfill the common requirements of consistency and diversity of augmentation across diverse scenarios. Evaluations across various datasets and tasks demonstrate the generality and efficiency of the proposed GOUDA over existing state-of-the-art GCLs.

The field of graph learning has been substantially advanced by the development of deep learning models, in particular graph neural networks. However, one salient yet largely under-explored challenge is detecting Out-of-Distribution (OOD) nodes on graphs. Prevailing OOD detection techniques developed in other domains like computer vision, do not cater to the interconnected nature of graphs. This work aims to fill this gap by exploring the potential of a simple yet effective method -- OOD score propagation, which propagates OOD scores among neighboring nodes along the graph structure. This post hoc solution can be easily integrated with existing OOD scoring functions, showcasing its excellent flexibility and effectiveness in most scenarios. However, the conditions under which score propagation proves beneficial remain not fully elucidated. Our study meticulously derives these conditions and, inspired by this discovery, introduces an innovative edge augmentation strategy with theoretical guarantee. Empirical evaluations affirm the superiority of our proposed method, outperforming strong OOD detection baselines in various scenarios and settings.