World models (WMs) demonstrate strong capabilities in prediction, generation, and planning tasks. Existing WMs primarily focus on unstructured data and cannot leverage the ubiquitous structured data, often represented as graphs, in the digital world. While multiple graph foundation models have been proposed, they focus on graph learning tasks and cannot extend to diverse multi-modal data and interdisciplinary tasks. To address these challenges, we propose the Graph World Model (GWM), a world model that supports both unstructured and graph-structured states with multi-modal information and represents diverse tasks as actions. The core of a GWM is a generic message-passing algorithm to aggregate structured information, either over a unified multi-modal token space by converting multi-modal data into text (GWM-T) or a unified multi-modal embedding space by modality-specific encoders (GWM-E). Notably, GWM introduces action nodes to support diverse tasks, where action nodes are linked to other nodes via direct reference or similarity computation. Extensive experiments on six tasks from diverse domains, including multi-modal generation and matching, recommendation, graph prediction, multi-agent, retrieval-augmented generation, and planning and optimization, show that the same GWM outperforms or matches domain-specific baselines' performance, benefits from multi-hop structures, and demonstrates strong zero-shot/few-shot capabilities on unseen new tasks. Our code for GWM is released at https://github.com/ulab-uiuc/GWM.
Federated Graph Learning (FGL) combines the privacy-preserving capabilities of federated learning (FL) with the strong graph modeling capability of Graph Neural Networks (GNNs). Current research addresses subgraph-FL only from the structural perspective, neglecting the propagation of graph signals on spatial and spectral domains of the structure. From a spatial perspective, subgraph-FL introduces edge disconnections between clients, leading to disruptions in label signals and a degradation in the class knowledge of the global GNN. From a spectral perspective, spectral heterogeneity causes inconsistencies in signal frequencies across subgraphs, which makes local GNNs overfit the local signal propagation schemes. As a result, spectral client drifts occur, undermining global generalizability. To tackle the challenges, we propose a global knowledge repository to mitigate label signal disruption and a frequency alignment to address spectral client drifts. The combination of spatial and spectral strategies forms our framework S2FGL. Extensive experiments on multiple datasets demonstrate the superiority of S2FGL. The code is available at https://github.com/Wonder7racer/S2FGL.git.
Recent advances in graph databases (GDBs) have been driving interest in large-scale analytics, yet current systems fail to support higher-order (HO) interactions beyond first-order (one-hop) relations, which are crucial for tasks such as subgraph counting, polyadic modeling, and HO graph learning. We address this by introducing a new class of systems, higher-order graph databases (HO-GDBs) that use lifting and lowering paradigms to seamlessly extend traditional GDBs with HO. We provide a theoretical analysis of OLTP and OLAP queries, ensuring correctness, scalability, and ACID compliance. We implement a lightweight, modular, and parallelizable HO-GDB prototype that offers native support for hypergraphs, node-tuples, subgraphs, and other HO structures under a unified API. The prototype scales to large HO OLTP & OLAP workloads and shows how HO improves analytical tasks, for example enhancing accuracy of graph neural networks within a GDB by 44%. Our work ensures low latency and high query throughput, and generalizes both ACID-compliant and eventually consistent systems.
Inspired by the success of large language models (LLMs), there is a significant research shift from traditional graph learning methods to LLM-based graph frameworks, formally known as GraphLLMs. GraphLLMs leverage the reasoning power of LLMs by integrating three key components: the textual attributes of input nodes, the structural information of node neighborhoods, and task-specific prompts that guide decision-making. Despite their promise, the robustness of GraphLLMs against adversarial perturbations remains largely unexplored-a critical concern for deploying these models in high-stakes scenarios. To bridge the gap, we introduce TrustGLM, a comprehensive study evaluating the vulnerability of GraphLLMs to adversarial attacks across three dimensions: text, graph structure, and prompt manipulations. We implement state-of-the-art attack algorithms from each perspective to rigorously assess model resilience. Through extensive experiments on six benchmark datasets from diverse domains, our findings reveal that GraphLLMs are highly susceptible to text attacks that merely replace a few semantically similar words in a node's textual attribute. We also find that standard graph structure attack methods can significantly degrade model performance, while random shuffling of the candidate label set in prompt templates leads to substantial performance drops. Beyond characterizing these vulnerabilities, we investigate defense techniques tailored to each attack vector through data-augmented training and adversarial training, which show promising potential to enhance the robustness of GraphLLMs. We hope that our open-sourced library will facilitate rapid, equitable evaluation and inspire further innovative research in this field.
Equivariant Graph Neural Networks (GNNs) have achieved remarkable success across diverse scientific applications. However, existing approaches face critical efficiency challenges when scaling to large geometric graphs and suffer significant performance degradation when the input graphs are sparsified for computational tractability. To address these limitations, we introduce FastEGNN and DistEGNN, two novel enhancements to equivariant GNNs for large-scale geometric graphs. FastEGNN employs a key innovation: a small ordered set of virtual nodes that effectively approximates the large unordered graph of real nodes. Specifically, we implement distinct message passing and aggregation mechanisms for different virtual nodes to ensure mutual distinctiveness, and minimize Maximum Mean Discrepancy (MMD) between virtual and real coordinates to achieve global distributedness. This design enables FastEGNN to maintain high accuracy while efficiently processing large-scale sparse graphs. For extremely large-scale geometric graphs, we present DistEGNN, a distributed extension where virtual nodes act as global bridges between subgraphs in different devices, maintaining consistency while dramatically reducing memory and computational overhead. We comprehensively evaluate our models across four challenging domains: N-body systems (100 nodes), protein dynamics (800 nodes), Water-3D (8,000 nodes), and our new Fluid113K benchmark (113,000 nodes). Results demonstrate superior efficiency and performance, establishing new capabilities in large-scale equivariant graph learning. Code is available at https://github.com/GLAD-RUC/DistEGNN.
We present LaplaceGNN, a novel self-supervised graph learning framework that bypasses the need for negative sampling by leveraging spectral bootstrapping techniques. Our method integrates Laplacian-based signals into the learning process, allowing the model to effectively capture rich structural representations without relying on contrastive objectives or handcrafted augmentations. By focusing on positive alignment, LaplaceGNN achieves linear scaling while offering a simpler, more efficient, self-supervised alternative for graph neural networks, applicable across diverse domains. Our contributions are twofold: we precompute spectral augmentations through max-min centrality-guided optimization, enabling rich structural supervision without relying on handcrafted augmentations, then we integrate an adversarial bootstrapped training scheme that further strengthens feature learning and robustness. Our extensive experiments on different benchmark datasets show that LaplaceGNN achieves superior performance compared to state-of-the-art self-supervised graph methods, offering a promising direction for efficiently learning expressive graph representations.
Graph Neural Networks (GNNs) have achieved state-of-the-art performance in node classification tasks but struggle with label noise in real-world data. Existing studies on graph learning with label noise commonly rely on class-dependent label noise, overlooking the complexities of instance-dependent noise and falling short of capturing real-world corruption patterns. We introduce BeGIN (Benchmarking for Graphs with Instance-dependent Noise), a new benchmark that provides realistic graph datasets with various noise types and comprehensively evaluates noise-handling strategies across GNN architectures, noisy label detection, and noise-robust learning. To simulate instance-dependent corruptions, BeGIN introduces algorithmic methods and LLM-based simulations. Our experiments reveal the challenges of instance-dependent noise, particularly LLM-based corruption, and underscore the importance of node-specific parameterization to enhance GNN robustness. By comprehensively evaluating noise-handling strategies, BeGIN provides insights into their effectiveness, efficiency, and key performance factors. We expect that BeGIN will serve as a valuable resource for advancing research on label noise in graphs and fostering the development of robust GNN training methods. The code is available at https://github.com/kimsu55/BeGIN.
Heterogeneous graph neural networks (HGNNs) excel at capturing structural and semantic information in heterogeneous graphs (HGs), while struggling to generalize across domains and tasks. Recently, some researchers have turned to integrating HGNNs with large language models (LLMs) for more generalizable heterogeneous graph learning. However, these approaches typically extract structural information via HGNNs as HG tokens, and disparities in embedding spaces between HGNNs and LLMs have been shown to bias the LLM's comprehension of HGs. Moreover, as these HG tokens are often derived from node-level tasks, the model's ability to generalize across tasks remains limited. To this end, we propose a simple yet effective Masked Language Modeling-based method, called MLM4HG. MLM4HG introduces metapath-based textual sequences instead of HG tokens to extract structural and semantic information inherent in HGs, and designs customized textual templates to unify different graph tasks into a coherent cloze-style "mask" token prediction paradigm. Specifically, MLM4HG first converts HGs from various domains to texts based on metapaths, and subsequently combines them with the unified task texts to form a HG-based corpus. Moreover, the corpus is fed into a pretrained LM for fine-tuning with a constrained target vocabulary, enabling the fine-tuned LM to generalize to unseen target HGs. Extensive cross-domain and multi-task experiments on four real-world datasets demonstrate the superior generalization performance of MLM4HG over state-of-the-art methods in both few-shot and zero-shot scenarios. Our code is available at https://github.com/BUPT-GAMMA/MLM4HG.
Graph learning has been crucial to many real-world tasks, but they are often studied with a closed-world assumption, with all possible labels of data known a priori. To enable effective graph learning in an open and noisy environment, it is critical to inform the model users when the model makes a wrong prediction to in-distribution data of a known class, i.e., misclassification detection or when the model encounters out-of-distribution from novel classes, i.e., out-of-distribution detection. This paper introduces Evidential Reasoning Network (EVINET), a framework that addresses these two challenges by integrating Beta embedding within a subjective logic framework. EVINET includes two key modules: Dissonance Reasoning for misclassification detection and Vacuity Reasoning for out-of-distribution detection. Extensive experiments demonstrate that EVINET outperforms state-of-the-art methods across multiple metrics in the tasks of in-distribution classification, misclassification detection, and out-of-distribution detection. EVINET demonstrates the necessity of uncertainty estimation and logical reasoning for misclassification detection and out-of-distribution detection and paves the way for open-world graph learning. Our code and data are available at https://github.com/SSSKJ/EviNET.
Existing graph benchmarks assume non-spatial, simple edges, collapsing physically distinct paths into a single link. We introduce HSG-12M, the first large-scale dataset of $\textbf{spatial multigraphs}-$graphs embedded in a metric space where multiple geometrically distinct trajectories between two nodes are retained as separate edges. HSG-12M contains 11.6 million static and 5.1 million dynamic $\textit{Hamiltonian spectral graphs}$ across 1401 characteristic-polynomial classes, derived from 177 TB of spectral potential data. Each graph encodes the full geometry of a 1-D crystal's energy spectrum on the complex plane, producing diverse, physics-grounded topologies that transcend conventional node-coordinate datasets. To enable future extensions, we release $\texttt{Poly2Graph}$: a high-performance, open-source pipeline that maps arbitrary 1-D crystal Hamiltonians to spectral graphs. Benchmarks with popular GNNs expose new challenges in learning from multi-edge geometry at scale. Beyond its practical utility, we show that spectral graphs serve as universal topological fingerprints of polynomials, vectors, and matrices, forging a new algebra-to-graph link. HSG-12M lays the groundwork for geometry-aware graph learning and new opportunities of data-driven scientific discovery in condensed matter physics and beyond.
The identification of drug-target interactions (DTI) is crucial for drug discovery and repositioning, as it reveals potential uses of existing drugs, aiding in the acceleration of the drug development process and reducing associated costs. Despite the similarity information in DTI is important, most models are limited to mining direct similarity information within homogeneous graphs, overlooking the potential yet rich similarity information in heterogeneous graphs. Inspired by real-world social interaction behaviors, we propose SOC-DGL, which comprises two specialized modules: the Affinity-Driven Graph Learning (ADGL) module and the Equilibrium-Driven Graph Learning (EDGL) module. The ADGL module adopts a comprehensive social interaction strategy, leveraging an affinity-enhanced global drug-target graph to learn both global DTI and the individual similarity information of drugs and targets. In contrast, the EDGL module employs a higher-order social interaction strategy, amplifying the influence of even-hop neighbors through an even-polynomial graph filter grounded in balance theory, enabling the indirect mining of higher-order homogeneous information. This dual approach enables SOC-DGL to effectively and comprehensively capture similarity information across diverse interaction scales within the affinity matrices and drug-target association matrices, significantly enhancing the model's generalization capability and predictive accuracy in DTI tasks. To address the issue of imbalance in drug-target interaction datasets, this paper proposes an adjustable imbalance loss function that mitigates the impact of sample imbalance by adjusting the weight of negative samples and a parameter. Extensive experiments on four benchmark datasets demonstrate significant accuracy improvements achieved by SOC-DGL, particularly in scenarios involving data imbalance and unseen drugs or targets.
Self-supervised topological deep learning (TDL) represents a nascent but underexplored area with significant potential for modeling higher-order interactions in simplicial complexes and cellular complexes to derive representations of unlabeled graphs. Compared to simplicial complexes, cellular complexes exhibit greater expressive power. However, the advancement in self-supervised learning for cellular TDL is largely hindered by two core challenges: \textit{extrinsic structural constraints} inherent to cellular complexes, and intrinsic semantic redundancy in cellular representations. The first challenge highlights that traditional graph augmentation techniques may compromise the integrity of higher-order cellular interactions, while the second underscores that topological redundancy in cellular complexes potentially diminish task-relevant information. To address these issues, we introduce Cellular Complex Contrastive Learning with Adaptive Trimming (CellCLAT), a twofold framework designed to adhere to the combinatorial constraints of cellular complexes while mitigating informational redundancy. Specifically, we propose a parameter perturbation-based augmentation method that injects controlled noise into cellular interactions without altering the underlying cellular structures, thereby preserving cellular topology during contrastive learning. Additionally, a cellular trimming scheduler is employed to mask gradient contributions from task-irrelevant cells through a bi-level meta-learning approach, effectively removing redundant topological elements while maintaining critical higher-order semantics. We provide theoretical justification and empirical validation to demonstrate that CellCLAT achieves substantial improvements over existing self-supervised graph learning methods, marking a significant attempt in this domain.
Agent-Based Models (ABMs) are powerful tools for studying emergent properties in complex systems. In ABMs, agent behaviors are governed by local interactions and stochastic rules. However, these rules are, in general, non-differentiable, limiting the use of gradient-based methods for optimization, and thus integration with real-world data. We propose a novel framework to learn a differentiable surrogate of any ABM by observing its generated data. Our method combines diffusion models to capture behavioral stochasticity and graph neural networks to model agent interactions. Distinct from prior surrogate approaches, our method introduces a fundamental shift: rather than approximating system-level outputs, it models individual agent behavior directly, preserving the decentralized, bottom-up dynamics that define ABMs. We validate our approach on two ABMs (Schelling's segregation model and a Predator-Prey ecosystem) showing that it replicates individual-level patterns and accurately forecasts emergent dynamics beyond training. Our results demonstrate the potential of combining diffusion models and graph learning for data-driven ABM simulation.
Graphs are a widely used paradigm for representing non-Euclidean data, with applications ranging from social network analysis to biomolecular prediction. Conventional graph learning approaches typically rely on fixed structural assumptions or fully observed data, limiting their effectiveness in more complex, noisy, or evolving settings. Consequently, real-world graph data often violates the assumptions of traditional graph learning methods, in particular, it leads to four fundamental challenges: (1) Incompleteness, real-world graphs have missing nodes, edges, or attributes; (2) Imbalance, the distribution of the labels of nodes or edges and their structures for real-world graphs are highly skewed; (3) Cross-domain Heterogeneity, graphs from different domains exhibit incompatible feature spaces or structural patterns; and (4) Dynamic Instability, graphs evolve over time in unpredictable ways. Recent advances in Large Language Models (LLMs) offer the potential to tackle these challenges by leveraging rich semantic reasoning and external knowledge. This survey provides a comprehensive review of how LLMs can be integrated with graph learning to address the aforementioned challenges. For each challenge, we review both traditional solutions and modern LLM-driven approaches, highlighting how LLMs contribute unique advantages. Finally, we discuss open research questions and promising future directions in this emerging interdisciplinary field. To support further exploration, we have curated a repository of recent advances on graph learning challenges: https://github.com/limengran98/Awesome-Literature-Graph-Learning-Challenges.
Graph neural networks (GNNs) has been predominantly driven by message-passing, where node representations are iteratively updated via local neighborhood aggregation. Despite their success, message-passing suffers from fundamental limitations -- including constrained expressiveness, over-smoothing, over-squashing, and limited capacity to model long-range dependencies. These issues hinder scalability: increasing data size or model size often fails to yield improved performance, limiting the viability of GNNs as backbones for graph foundation models. In this work, we explore pathways beyond message-passing and introduce Generative Graph Pattern Machine (G$^2$PM), a generative Transformer pre-training framework for graphs. G$^2$PM represents graph instances (nodes, edges, or entire graphs) as sequences of substructures, and employs generative pre-training over the sequences to learn generalizable, transferable representations. Empirically, G$^2$PM demonstrates strong scalability: on the ogbn-arxiv benchmark, it continues to improve with model sizes up to 60M parameters, outperforming prior generative approaches that plateau at significantly smaller scales (e.g., 3M). In addition, we systematically analyze the model design space, highlighting key architectural choices that contribute to its scalability and generalization. Across diverse tasks -- including node classification, graph classification, and transfer learning -- G$^2$PM consistently outperforms strong baselines, establishing a compelling foundation for scalable graph learning. The code and dataset are available at https://github.com/Zehong-Wang/G2PM.
Recent advances in graph machine learning (ML) with the introduction of Graph Neural Networks (GNNs) have led to a widespread interest in applying these approaches to business applications at scale. GNNs enable differentiable end-to-end (E2E) learning of model parameters given graph structure which enables optimization towards popular node, edge (link) and graph-level tasks. While the research innovation in new GNN layers and training strategies has been rapid, industrial adoption and utility of GNNs has lagged considerably due to the unique scale challenges that large-scale graph ML problems create. In this work, we share our approach to training, inference, and utilization of GNNs at Snapchat. To this end, we present GiGL (Gigantic Graph Learning), an open-source library to enable large-scale distributed graph ML to the benefit of researchers, ML engineers, and practitioners. We use GiGL internally at Snapchat to manage the heavy lifting of GNN workflows, including graph data preprocessing from relational DBs, subgraph sampling, distributed training, inference, and orchestration. GiGL is designed to interface cleanly with open-source GNN modeling libraries prominent in academia like PyTorch Geometric (PyG), while handling scaling and productionization challenges that make it easier for internal practitioners to focus on modeling. GiGL is used in multiple production settings, and has powered over 35 launches across multiple business domains in the last 2 years in the contexts of friend recommendation, content recommendation and advertising. This work details high-level design and tools the library provides, scaling properties, case studies in diverse business settings with industry-scale graphs, and several key lessons learned in employing graph ML at scale on large social data. GiGL is open-sourced at https://github.com/snap-research/GiGL.
Graph-structured data pervades domains such as social networks, biological systems, knowledge graphs, and recommender systems. While foundation models have transformed natural language processing, vision, and multimodal learning through large-scale pretraining and generalization, extending these capabilities to graphs -- characterized by non-Euclidean structures and complex relational semantics -- poses unique challenges and opens new opportunities. To this end, Graph Foundation Models (GFMs) aim to bring scalable, general-purpose intelligence to structured data, enabling broad transfer across graph-centric tasks and domains. This survey provides a comprehensive overview of GFMs, unifying diverse efforts under a modular framework comprising three key components: backbone architectures, pretraining strategies, and adaptation mechanisms. We categorize GFMs by their generalization scope -- universal, task-specific, and domain-specific -- and review representative methods, key innovations, and theoretical insights within each category. Beyond methodology, we examine theoretical foundations including transferability and emergent capabilities, and highlight key challenges such as structural alignment, heterogeneity, scalability, and evaluation. Positioned at the intersection of graph learning and general-purpose AI, GFMs are poised to become foundational infrastructure for open-ended reasoning over structured data. This survey consolidates current progress and outlines future directions to guide research in this rapidly evolving field. Resources are available at https://github.com/Zehong-Wang/Awesome-Foundation-Models-on-Graphs.
To forecast traffic with both spatial and temporal dimensions, we unroll a mixed-graph-based optimization algorithm into a lightweight and interpretable transformer-like neural net. Specifically, we construct two graphs: an undirected graph $\mathcal{G}^u$ capturing spatial correlations across geography, and a directed graph $\mathcal{G}^d$ capturing sequential relationships over time. We formulate a prediction problem for the future samples of signal $\mathbf{x}$, assuming it is "smooth" with respect to both $\mathcal{G}^u$ and $\mathcal{G}^d$, where we design new $\ell_2$ and $\ell_1$-norm variational terms to quantify and promote signal smoothness (low-frequency reconstruction) on a directed graph. We construct an iterative algorithm based on alternating direction method of multipliers (ADMM), and unroll it into a feed-forward network for data-driven parameter learning. We insert graph learning modules for $\mathcal{G}^u$ and $\mathcal{G}^d$, which are akin to the self-attention mechanism in classical transformers. Experiments show that our unrolled networks achieve competitive traffic forecast performance as state-of-the-art prediction schemes, while reducing parameter counts drastically. Our code is available in https://github.com/SingularityUndefined/Unrolling-GSP-STForecast.
Large Language Models (LLMs) have achieved remarkable success across various domains. However, they still face significant challenges, including high computational costs for training and limitations in solving complex reasoning problems. Although existing methods have extended the reasoning capabilities of LLMs through structured paradigms, these approaches often rely on task-specific prompts and predefined reasoning processes, which constrain their flexibility and generalizability. To address these limitations, we propose a novel framework that leverages graph learning to enable more flexible and adaptive reasoning capabilities for LLMs. Specifically, this approach models the reasoning process of a problem as a graph and employs LLM-based graph learning to guide the adaptive generation of each reasoning step. To further enhance the adaptability of the model, we introduce a Graph Neural Network (GNN) module to perform representation learning on the generated reasoning process, enabling real-time adjustments to both the model and the prompt. Experimental results demonstrate that this method significantly improves reasoning performance across multiple tasks without requiring additional training or task-specific prompt design. Code can be found in https://github.com/zch65458525/L2T.
Partial label learning (PLL) is a significant weakly supervised learning framework, where each training example corresponds to a set of candidate labels and only one label is the ground-truth label. For the first time, this paper investigates the partial label clustering problem, which takes advantage of the limited available partial labels to improve the clustering performance. Specifically, we first construct a weight matrix of examples based on their relationships in the feature space and disambiguate the candidate labels to estimate the ground-truth label based on the weight matrix. Then, we construct a set of must-link and cannot-link constraints based on the disambiguation results. Moreover, we propagate the initial must-link and cannot-link constraints based on an adversarial prior promoted dual-graph learning approach. Finally, we integrate weight matrix construction, label disambiguation, and pairwise constraints propagation into a joint model to achieve mutual enhancement. We also theoretically prove that a better disambiguated label matrix can help improve clustering performance. Comprehensive experiments demonstrate our method realizes superior performance when comparing with state-of-the-art constrained clustering methods, and outperforms PLL and semi-supervised PLL methods when only limited samples are annotated. The code is publicly available at https://github.com/xyt-ml/PLC.