NeurIPS 2024 Papers

Extensive knowledge graphs (KGs) have been constructed to facilitate knowledge-driven tasks across various scenarios. However, existing work usually develops separate reasoning models for different KGs, lacking the ability to generalize and transfer knowledge across diverse KGs and reasoning settings. In this paper, we propose a prompt-based KG foundation model via in-context learning, namely KG-ICL, to achieve a universal reasoning ability. Specifically, we introduce a prompt graph centered with a query-related example fact as context to understand the query relation. To encode prompt graphs with the generalization ability to unseen entities and relations in queries, we first propose a unified tokenizer that maps entities and relations in prompt graphs to predefined tokens. Then, we propose two message passing neural networks to perform prompt encoding and KG reasoning, respectively. We conduct evaluation on 43 different KGs in both transductive and inductive settings. Results indicate that the proposed KG-ICL outperforms baselines on most datasets, showcasing its outstanding generalization and universal reasoning capabilities. The source code is accessible on GitHub: https://github.com/nju-websoft/KG-ICL.

Graph neural networks (GNNs) have become the dominant solution for learning on graphs, the typical non-Euclidean structures. Conventional GNNs, constructed with the Artificial Neuron Network (ANN), have achieved impressive performance at the cost of high computation and energy consumption. In parallel, spiking GNNs with brain-like spiking neurons are drawing increasing research attention owing to the energy efficiency. So far, existing spiking GNNs consider graphs in Euclidean space, ignoring the structural geometry, and suffer from the high latency issue due to Back-Propagation-Through-Time (BPTT) with the surrogate gradient. In light of the aforementioned issues, we are devoted to exploring spiking GNN on Riemannian manifolds, and present a Manifold-valued Spiking GNN (MSG). In particular, we design a new spiking neuron on geodesically complete manifolds with the diffeomorphism, so that BPTT regarding the spikes is replaced by the proposed differentiation via manifold. Theoretically, we show that MSG approximates a solver of the manifold ordinary differential equation. Extensive experiments on common graphs show the proposed MSG achieves superior performance to previous spiking GNNs and energy efficiency to conventional GNNs.

Temporal Knowledge Graph (TKG) representation learning aims to map temporal evolving entities and relations to embedded representations in a continuous low-dimensional vector space. However, existing approaches cannot capture the temporal evolution of high-order correlations in TKGs. To this end, we propose a **D**eep **E**volutionary **C**lustering jointed temporal knowledge graph **R**epresentation **L**earning approach (**DECRL**). Specifically, a deep evolutionary clustering module is proposed to capture the temporal evolution of high-order correlations among entities. Furthermore, a cluster-aware unsupervised alignment mechanism is introduced to ensure the precise one-to-one alignment of soft overlapping clusters across timestamps, thereby maintaining the temporal smoothness of clusters. In addition, an implicit correlation encoder is introduced to capture latent correlations between any pair of clusters under the guidance of a global graph. Extensive experiments on seven real-world datasets demonstrate that DECRL achieves the state-of-the-art performances, outperforming the best baseline by an average of 9.53\%, 12.98\%, 10.42\%, and 14.68\% in MRR, Hits@1, Hits@3, and Hits@10, respectively.

Over the past few years, research on deep graph learning has shifted from static graphs to temporal graphs in response to real-world complex systems that exhibit dynamic behaviors. In practice, temporal graphs are formalized as an ordered sequence of static graph snapshots observed at discrete time points. Sequence models such as RNNs or Transformers have long been the predominant backbone networks for modeling such temporal graphs. Yet, despite the promising results, RNNs struggle with long-range dependencies, while transformers are burdened by quadratic computational complexity. Recently, state space models (SSMs), which are framed as discretized representations of an underlying continuous-time linear dynamical system, have garnered substantial attention and achieved breakthrough advancements in independent sequence modeling. In this work, we undertake a principled investigation that extends SSM theory to temporal graphs by integrating structural information into the online approximation objective via the adoption of a Laplacian regularization term. The emergent continuous-time system introduces novel algorithmic challenges, thereby necessitating our development of GraphSSM, a graph state space model for modeling the dynamics of temporal graphs. Extensive experimental results demonstrate the effectiveness of our GraphSSM framework across various temporal graph benchmarks.

Cross-domain recommendation (CDR) offers a promising solution to the data sparsity problem by enabling knowledge transfer across source and target domains. However, many recent CDR models overlook crucial issues such as privacy as well as the risk of negative transfer (which negatively impact model performance), especially in multi-domain settings. To address these challenges, we propose FedGCDR, a novel federated graph learning framework that securely and effectively leverages positive knowledge from multiple source domains. First, we design a positive knowledge transfer module that ensures privacy during inter-domain knowledge transmission. This module employs differential privacy-based knowledge extraction combined with a feature mapping mechanism, transforming source domain embeddings from federated graph attention networks into reliable domain knowledge. Second, we design a knowledge activation module to filter out potential harmful or conflicting knowledge from source domains, addressing the issues of negative transfer. This module enhances target domain training by expanding the graph of the target domain to generate reliable domain attentions and fine-tunes the target model for improved negative knowledge filtering and more accurate predictions. We conduct extensive experiments on 16 popular domains of the Amazon dataset, demonstrating that FedGCDR significantly outperforms state-of-the-art methods.

Graph transformers need strong inductive biases to derive meaningful attention scores. Yet, current methods often fall short in capturing longer ranges, hierarchical structures, or community structures, which are common in various graphs such as molecules, social networks, and citation networks. This paper presents a Hierarchical Distance Structural Encoding (HDSE) method to model node distances in a graph, focusing on its multi-level, hierarchical nature. We introduce a novel framework to seamlessly integrate HDSE into the attention mechanism of existing graph transformers, allowing for simultaneous application with other positional encodings. To apply graph transformers with HDSE to large-scale graphs, we further propose a high-level HDSE that effectively biases the linear transformers towards graph hierarchies. We theoretically prove the superiority of HDSE in terms of expressivity and generalization. Empirically, we demonstrate that graph transformers with HDSE excel in graph classification, regression on 7 graph-level datasets, and node classification on 11 large-scale graphs.

Temporal link prediction, aiming at predicting future interactions among entities based on historical interactions, is crucial for a series of real-world applications. Although previous methods have demonstrated the importance of relative encodings for effective temporal link prediction, computational efficiency remains a major concern in constructing these encodings. Moreover, existing relative encodings are usually constructed based on structural connectivity, where temporal information is seldom considered. To address the aforementioned issues, we first analyze existing relative encodings and unify them as a function of temporal walk matrices. This unification establishes a connection between relative encodings and temporal walk matrices, providing a more principled way for analyzing and designing relative encodings. Based on this analysis, we propose a new temporal graph neural network called TPNet, which introduces a temporal walk matrix that incorporates the time decay effect to simultaneously consider both temporal and structural information. Moreover, TPNet designs a random feature propagation mechanism with theoretical guarantees to implicitly maintain the temporal walk matrices, which improves the computation and storage efficiency. Experimental results on 13 benchmark datasets verify the effectiveness and efficiency of TPNet, where TPNet outperforms other baselines on most datasets and achieves a maximum speedup of $33.3 \times$ compared to the SOTA baseline.

In this work we design graph neural network architectures that capture optimal approximation algorithms for a large class of combinatorial optimization problems, using powerful algorithmic tools from semidefinite programming (SDP). Concretely, we prove that polynomial-sized message-passing algorithms can represent the most powerful polynomial time algorithms for Max Constraint Satisfaction Problems assuming the Unique Games Conjecture. We leverage this result to construct efficient graph neural network architectures, OptGNN, that obtain high quality approximate solutions on landmark combinatorial optimization problems such as Max-Cut, Min-Vertex-Cover, and Max-3-SAT. Our approach achieves strong empirical results across a wide range of real-world and synthetic datasets against solvers and neural baselines. Finally, we take advantage of OptGNN’s ability to capture convex relaxations to design an algorithm for producing bounds on the optimal solution from the learned embeddings of OptGNN.

Neural Algorithmic Reasoning (NAR) research has demonstrated that graph neural networks (GNNs) could learn to execute classical algorithms. However, most previous approaches have always used a recurrent architecture, where each iteration of the GNN matches an iteration of the algorithm. In this paper we study neurally solving algorithms from a different perspective: since the algorithm’s solution is often an equilibrium, it is possible to find the solution directly by solving an equilibrium equation. Our approach requires no information on the ground-truth number of steps of the algorithm, both during train and test time. Furthermore, the proposed method improves the performance of GNNs on executing algorithms and is a step towards speeding up existing NAR models. Our empirical evidence, leveraging algorithms from the CLRS-30 benchmark, validates that one can train a network to solve algorithmic problems by directly finding the equilibrium. We discuss the practical implementation of such models and propose regularisations to improve the performance of these equilibrium reasoners.

Out-of-distribution (OOD) generalization issue is a well-known challenge within deep learning tasks. In dynamic graphs, the change of temporal environments is regarded as the main cause of data distribution shift. While numerous OOD studies focusing on environment factors have achieved remarkable performance, they still fail to systematically solve the two issue of environment inference and utilization. In this work, we propose a novel dynamic graph learning model named EpoD based on prompt learning and structural causal model to comprehensively enhance both environment inference and utilization. Inspired by the superior performance of prompt learning in understanding underlying semantic and causal associations, we first design a self-prompted learning mechanism to infer unseen environment factors. We then rethink the role of environment variable within spatio-temporal causal structure model, and introduce a novel causal pathway where dynamic subgraphs serve as mediating variables. The extracted dynamic subgraph can effectively capture the data distribution shift by incorporating the inferred environment variables into the node-wise dependencies. Theoretical discussions and intuitive analysis support the generalizability and interpretability of EpoD. Extensive experiments on seven real-world datasets across domains showcase the superiority of EpoD against baselines, and toy example experiments further verify the powerful interpretability and rationality of our EpoD.

Graph Contrastive Learning (GCL) has emerged as a powerful approach for generating graph representations without the need for manual annotation. Most advanced GCL methods fall into three main frameworks: node discrimination, group discrimination, and bootstrapping schemes, all of which achieve comparable performance. However, the underlying mechanisms and factors that contribute to their effectiveness are not yet fully understood. In this paper, we revisit these frameworks and reveal a common mechanism—representation scattering—that significantly enhances their performance. Our discovery highlights an essential feature of GCL and unifies these seemingly disparate methods under the concept of representation scattering. To leverage this insight, we introduce Scattering Graph Representation Learning (SGRL), a novel framework that incorporates a new representation scattering mechanism designed to enhance representation diversity through a center-away strategy. Additionally, consider the interconnected nature of graphs, we develop a topology-based constraint mechanism that integrates graph structural properties with representation scattering to prevent excessive scattering. We extensively evaluate SGRL across various downstream tasks on benchmark datasets, demonstrating its efficacy and superiority over existing GCL methods. Our findings underscore the significance of representation scattering in GCL and provide a structured framework for harnessing this mechanism to advance graph representation learning. The code of SGRL is at https://github.com/hedongxiao-tju/SGRL.

Graph data are inherently complex and heterogeneous, leading to a high natural diversity of distributional shifts. However, it remains unclear how to build machine learning architectures that generalize to the complex distributional shifts naturally occurring in the real world. Here, we develop GraphMETRO, a Graph Neural Network architecture that models natural diversity and captures complex distributional shifts. GraphMETRO employs a Mixture-of-Experts (MoE) architecture with a gating model and multiple expert models, where each expert model targets a specific distributional shift to produce a referential representation w.r.t. a reference model, and the gating model identifies shift components. Additionally, we design a novel objective that aligns the representations from different expert models to ensure reliable optimization. GraphMETRO achieves state-of-the-art results on four datasets from the GOOD benchmark, which is comprised of complex and natural real-world distribution shifts, improving by 67% and 4.2% on the WebKB and Twitch datasets. Code and data are available at https://github.com/Wuyxin/GraphMETRO.

Simulating large scenes with many rigid objects is crucial for a variety of applications, such as robotics, engineering, film and video games. Rigid interactions are notoriously hard to model: small changes to the initial state or the simulation parameters can lead to large changes in the final state. Recently, learned simulators based on graph networks (GNNs) were developed as an alternative to hand-designed simulators like MuJoCo and Bullet. They are able to accurately capture dynamics of real objects directly from real-world observations. However, current state-of-the-art learned simulators operate on meshes and scale poorly to scenes with many objects or detailed shapes. Here we present SDF-Sim, the first learned rigid-body simulator designed for scale. We use learned signed-distance functions (SDFs) to represent the object shapes and to speed up distance computation. We design the simulator to leverage SDFs and avoid the fundamental bottleneck of the previous simulators associated with collision detection. For the first time in literature, we demonstrate that we can scale the GNN-based simulators to scenes with hundreds of objects and up to 1.1 million nodes, where mesh-based approaches run out of memory. Finally, we show that SDF-Sim can be applied to real world scenes by extracting SDFs from multi-view images.

Due to its low storage cost and fast search speed, cross-modal retrieval based on hashing has attracted widespread attention and is widely used in real-world applications of social media search. However, most existing hashing methods are often limited by uncomprehensive feature representations and semantic associations, which greatly restricts their performance and applicability in practical applications. To deal with this challenge, in this paper, we propose an end-to-end graph attention network hashing (EGATH) for cross-modal retrieval, which can not only capture direct semantic associations between images and texts but also match semantic content between different modalities. We adopt the contrastive language image pretraining (CLIP) combined with the Transformer to improve understanding and generalization ability in semantic consistency across different data modalities. The classifier based on graph attention network is applied to obtain predicted labels to enhance cross-modal feature representation. We construct hash codes using an optimization strategy and loss function to preserve the semantic information and compactness of the hash code. Comprehensive experiments on the NUS-WIDE, MIRFlickr25K, and MS-COCO benchmark datasets show that our EGATH significantly outperforms against several state-of-the-art methods.

Graph neural networks (GNNs) have been analyzed from multiple perspectives, including the WL-hierarchy, which exposes limits on their expressivity to distinguish graphs. However, characterizing the class of functions that they learn has remained unresolved. We address this fundamental question for message passing GNNs under ReLU activations, i.e., the de-facto choice for most GNNs. We first show that such GNNs learn tropical rational signomial maps or continuous piecewise linear functions, establishing an equivalence with feedforward networks (FNNs). We then elucidate the role of the choice of aggregation and update functions, and derive the first general upper and lower bounds on the geometric complexity (i.e., the number of linear regions), establishing new results for popular architectures such as GraphSAGE and GIN. We also introduce and theoretically analyze several new architectures to illuminate the relative merits of the feedforward and the message passing layers, and the tradeoffs involving depth and number of trainable parameters. Finally, we also characterize the decision boundary for node and graph classification tasks.

Label Distribution Learning (LDL) has been extensively studied in IID data applications such as computer vision, thanks to its more generic setting over single-label and multi-label classification. This paper advances LDL into graph domains and aims to tackle a novel and fundamental heterogeneous graph label distribution learning (HGDL) problem. We argue that the graph heterogeneity reflected on node types, node attributes, and neighborhood structures can impose significant challenges for generalizing LDL onto graphs. To address the challenges, we propose a new learning framework with two key components: 1) proactive graph topology homogenization, and 2) topology and content consistency-aware graph transformer. Specifically, the former learns optimal information aggregation between meta-paths, so that the node heterogeneity can be proactively addressed prior to the succeeding embedding learning; the latter leverages an attention mechanism to learn consistency between meta-path and node attributes, allowing network topology and nodal attributes to be equally emphasized during the label distribution learning. By using KL-divergence and additional constraints, \method~delivers an end-to-end solution for learning and predicting label distribution for nodes. Both theoretical and empirical studies substantiate the effectiveness of our HGDL approach. Our code and datasets are available at https://github.com/Listener-Watcher/HGDL.

Generative models have shown great promise in generating 3D geometric systems, which is a fundamental problem in many natural science domains such as molecule and protein design. However, existing approaches only operate on static structures, neglecting the fact that physical systems are always dynamic in nature. In this work, we propose geometric trajectory diffusion models (GeoTDM), the first diffusion model for modeling the temporal distribution of 3D geometric trajectories. Modeling such distribution is challenging as it requires capturing both the complex spatial interactions with physical symmetries and temporal correspondence encapsulated in the dynamics. We theoretically justify that diffusion models with equivariant temporal kernels can lead to density with desired symmetry, and develop a novel transition kernel leveraging SE(3)-equivariant spatial convolution and temporal attention. Furthermore, to induce an expressive trajectory distribution for conditional generation, we introduce a generalized learnable geometric prior into the forward diffusion process to enhance temporal conditioning. We conduct extensive experiments on both unconditional and conditional generation in various scenarios, including physical simulation, molecular dynamics, and pedestrian motion. Empirical results on a wide suite of metrics demonstrate that GeoTDM can generate realistic geometric trajectories with significantly higher quality.

Graph neural networks (GNNs) have recently emerged as powerful tools for addressing complex optimization problems. It has been theoretically demonstrated that GNNs can universally approximate the solution mapping functions of linear programming (LP) problems. However, these theoretical results typically require GNNs to have large parameter sizes. Conversely, empirical experiments have shown that relatively small GNNs can solve LPs effectively, revealing a significant discrepancy between theoretical predictions and practical observations. In this work, we aim to bridge this gap by providing a theoretical foundation for the effectiveness of small-size GNNs. We prove that polylogarithmic-depth, constant-width GNNs are sufficient to solve packing and covering LPs, two widely used classes of LPs. Our proof leverages the capability of GNNs to simulate a variant of the gradient descent algorithm on a carefully selected potential function. Additionally, we introduce a new GNN architecture, termed GD-Net. Experimental results demonstrate that GD-Net significantly outperforms conventional GNN structures while using fewer parameters.

Training high-quality deep models necessitates vast amounts of data, resulting in overwhelming computational and memory demands. Recently, data pruning, distillation, and coreset selection have been developed to streamline data volume by \textit{retaining}, \textit{synthesizing}, or \textit{selecting} a small yet informative subset from the full set. Among these methods, data pruning incurs the least additional training cost and offers the most practical acceleration benefits. However, it is the most vulnerable, often suffering significant performance degradation with imbalanced or biased data schema, thus raising concerns about its accuracy and reliability in on-device deployment. Therefore, there is a looming need for a new data pruning paradigm that maintains the efficiency of previous practices while ensuring balance and robustness. Unlike the fields of computer vision and natural language processing, where mature solutions have been developed to address these issues, graph neural networks (GNNs) continue to struggle with increasingly large-scale, imbalanced, and noisy datasets, lacking a unified dataset pruning solution. To achieve this, we introduce a novel dynamic soft-pruning method, \ourmethod, designed to update the training ``basket'' during the process using trainable prototypes. \ourmethod first constructs a well-modeled graph embedding hypersphere and then samples \textit{representative, balanced, and unbiased subsets} from this embedding space, which achieves the goal we called {\fontfamily{lmtt}\selectfont \textbf{Graph Training Debugging}}. Extensive experiments on four datasets across three GNN backbones, demonstrate that \ourmethod (I) achieves or surpasses the performance of the full dataset with $30\%\sim50\%$ fewer training samples, (II) attains up to a $2.81\times$ lossless training speedup, and (III) outperforms state-of-the-art pruning methods in imbalanced training and noisy training scenarios by $0.3\%\sim4.3\%$ and $3.6\%\sim7.8\%$, respectively.