Recommender systems (RecSys) are essential for online platforms, providing personalized suggestions to users within a vast sea of information. Self-supervised graph learning seeks to harness high-order collaborative filtering signals through unsupervised augmentation on the user-item bipartite graph, primarily leveraging a multi-task learning framework that includes both supervised recommendation loss and self-supervised contrastive loss. However, this separate design introduces additional graph convolution processes and creates inconsistencies in gradient directions due to disparate losses, resulting in prolonged training times and sub-optimal performance. In this study, we introduce a unified framework of Supervised Graph Contrastive Learning for recommendation (SGCL) to address these issues. SGCL uniquely combines the training of recommendation and unsupervised contrastive losses into a cohesive supervised contrastive learning loss, aligning both tasks within a single optimization direction for exceptionally fast training. Extensive experiments on three real-world datasets show that SGCL outperforms state-of-the-art methods, achieving superior accuracy and efficiency.
Accurately predicting drug-target interactions (DTIs) is pivotal for advancing drug discovery and target validation techniques. While machine learning approaches including those that are based on Graph Neural Networks (GNN) have achieved notable success in DTI prediction, many of them have difficulties in effectively integrating the diverse features of drugs, targets and their interactions. To address this limitation, we introduce a novel framework to take advantage of the power of both transductive learning and inductive learning so that features at molecular level and drug-target interaction network level can be exploited. Within this framework is a GNN-based model called Graph-in-Graph (GiG) that represents graphs of drug and target molecular structures as meta-nodes in a drug-target interaction graph, enabling a detailed exploration of their intricate relationships. To evaluate the proposed model, we have compiled a special benchmark comprising drug SMILES, protein sequences, and their interaction data, which is interesting in its own right. Our experimental results demonstrate that the GiG model significantly outperforms existing approaches across all evaluation metrics, highlighting the benefits of integrating different learning paradigms and interaction data.
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.
In traffic prediction, the goal is to estimate traffic speed or flow in specific regions or road segments using historical data collected by devices deployed in each area. Each region or road segment can be viewed as an individual client that measures local traffic flow, making Federated Learning (FL) a suitable approach for collaboratively training models without sharing raw data. In centralized FL, a central server collects and aggregates model updates from multiple clients to build a shared model while preserving each client's data privacy. Standard FL methods, such as Federated Averaging (FedAvg), assume that clients are independent, which can limit performance in traffic prediction tasks where spatial relationships between clients are important. Federated Graph Learning methods can capture these dependencies during server-side aggregation, but they often introduce significant computational overhead. In this paper, we propose a lightweight graph-aware FL approach that blends the simplicity of FedAvg with key ideas from graph learning. Rather than training full models, our method applies basic neighbourhood aggregation principles to guide parameter updates, weighting client models based on graph connectivity. This approach captures spatial relationships effectively while remaining computationally efficient. We evaluate our method on two benchmark traffic datasets, METR-LA and PEMS-BAY, and show that it achieves competitive performance compared to standard baselines and recent graph-based federated learning techniques.
Dynamic Text-Attributed Graphs (DyTAGs), which intricately integrate structural, temporal, and textual attributes, are crucial for modeling complex real-world systems. However, most of the existing DyTAG datasets exhibit poor textual quality, which severely limits their utility for DyTAG generation tasks requiring semantically rich inputs. Additionally, prior work mainly focuses on discriminative tasks on DyTAGs, resulting in a lack of standardized task formulations and evaluation protocols tailored for DyTAG generation. To address these critical issues, we propose Generative DyTAG Benchmark (GDGB), which comprises eight meticulously curated DyTAG datasets with high-quality textual features for both nodes and edges, overcoming limitations of prior datasets. Building on GDGB, we define two novel DyTAG generation tasks: Transductive Dynamic Graph Generation (TDGG) and Inductive Dynamic Graph Generation (IDGG). TDGG transductively generates a target DyTAG based on the given source and destination node sets, while the more challenging IDGG introduces new node generation to inductively model the dynamic expansion of real-world graph data. To enable holistic evaluation, we design multifaceted metrics that assess the structural, temporal, and textual quality of the generated DyTAGs. We further propose GAG-General, an LLM-based multi-agent generative framework tailored for reproducible and robust benchmarking of DyTAG generation. Experimental results demonstrate that GDGB enables rigorous evaluation of TDGG and IDGG, with key insights revealing the critical interplay of structural and textual features in DyTAG generation. These findings establish GDGB as a foundational resource for advancing generative DyTAG research and unlocking further practical applications in DyTAG generation. GDGB datasets, source codes, and leaderboards are available at \href{https://gdgb-algo.github.io/}{here}.
Graph learning has rapidly evolved into a critical subfield of machine learning and artificial intelligence (AI). Its development began with early graph-theoretic methods, gaining significant momentum with the advent of graph neural networks (GNNs). Over the past decade, progress in scalable architectures, dynamic graph modeling, multimodal learning, generative AI, explainable AI (XAI), and responsible AI has broadened the applicability of graph learning to various challenging environments. Graph learning is significant due to its ability to model complex, non-Euclidean relationships that traditional machine learning struggles to capture, thus better supporting real-world applications ranging from drug discovery and fraud detection to recommender systems and scientific reasoning. However, challenges like scalability, generalization, heterogeneity, interpretability, and trustworthiness must be addressed to unlock its full potential. This survey provides a comprehensive introduction to graph learning, focusing on key dimensions including scalable, temporal, multimodal, generative, explainable, and responsible graph learning. We review state-of-the-art techniques for efficiently handling large-scale graphs, capturing dynamic temporal dependencies, integrating heterogeneous data modalities, generating novel graph samples, and enhancing interpretability to foster trust and transparency. We also explore ethical considerations, such as privacy and fairness, to ensure responsible deployment of graph learning models. Additionally, we identify and discuss emerging topics, highlighting recent integration of graph learning and other AI paradigms and offering insights into future directions. This survey serves as a valuable resource for researchers and practitioners seeking to navigate the rapidly evolving landscape of graph learning.
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 research on deep graph learning has shifted from static to dynamic graphs, motivated by the evolving behaviors observed in complex real-world systems. However, the temporal extension in dynamic graphs poses significant data efficiency challenges, including increased data volume, high spatiotemporal redundancy, and reliance on costly dynamic graph neural networks (DGNNs). To alleviate the concerns, we pioneer the study of dynamic graph condensation (DGC), which aims to substantially reduce the scale of dynamic graphs for data-efficient DGNN training. Accordingly, we propose DyGC, a novel framework that condenses the real dynamic graph into a compact version while faithfully preserving the inherent spatiotemporal characteristics. Specifically, to endow synthetic graphs with realistic evolving structures, a novel spiking structure generation mechanism is introduced. It draws on the dynamic behavior of spiking neurons to model temporally-aware connectivity in dynamic graphs. Given the tightly coupled spatiotemporal dependencies, DyGC proposes a tailored distribution matching approach that first constructs a semantically rich state evolving field for dynamic graphs, and then performs fine-grained spatiotemporal state alignment to guide the optimization of the condensed graph. Experiments across multiple dynamic graph datasets and representative DGNN architectures demonstrate the effectiveness of DyGC. Notably, our method retains up to 96.2% DGNN performance with only 0.5% of the original graph size, and achieves up to 1846 times training speedup.
Concept-Based Models (CBMs) are a class of deep learning models that provide interpretability by explaining predictions through high-level concepts. These models first predict concepts and then use them to perform a downstream task. However, current CBMs offer interpretability only for the final task prediction, while the concept predictions themselves are typically made via black-box neural networks. To address this limitation, we propose Hierarchical Concept Memory Reasoner (H-CMR), a new CBM that provides interpretability for both concept and task predictions. H-CMR models relationships between concepts using a learned directed acyclic graph, where edges represent logic rules that define concepts in terms of other concepts. During inference, H-CMR employs a neural attention mechanism to select a subset of these rules, which are then applied hierarchically to predict all concepts and the final task. Experimental results demonstrate that H-CMR matches state-of-the-art performance while enabling strong human interaction through concept and model interventions. The former can significantly improve accuracy at inference time, while the latter can enhance data efficiency during training when background knowledge is available.
Graph Neural Networks (GNNs) have demonstrated impressive performance across diverse graph-based tasks by leveraging message passing to capture complex node relationships. However, when applied to large-scale real-world graphs, GNNs face two major challenges: First, it becomes increasingly difficult to ensure both scalability and efficiency, as the repeated aggregation of large neighborhoods leads to significant computational overhead; Second, the over-smoothing problem arises, where excessive or deep propagation makes node representations indistinguishable, severely hindering model expressiveness. To tackle these issues, we propose ScaleGNN, a novel framework that adaptively fuses multi-hop node features for both scalable and effective graph learning. First, we construct per-hop pure neighbor matrices that capture only the exclusive structural information at each hop, avoiding the redundancy of conventional aggregation. Then, an enhanced feature fusion strategy significantly balances low-order and high-order information, preserving both local detail and global correlations without incurring excessive complexity. To further reduce redundancy and over-smoothing, we introduce a Local Contribution Score (LCS)-based masking mechanism to filter out less relevant high-order neighbors, ensuring that only the most meaningful information is aggregated. In addition, learnable sparse constraints selectively integrate multi-hop valuable features, emphasizing the most informative high-order neighbors. Extensive experiments on real-world datasets demonstrate that ScaleGNN consistently outperforms state-of-the-art GNNs in both predictive accuracy and computational efficiency, highlighting its practical value for large-scale graph learning.
Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with noisy data, limited scalability, and inadequate modelling of complex cellular relationships. We present SemanticST, a biologically informed, graph-based deep learning framework that models diverse cellular contexts through multi-semantic graph construction. SemanticST builds multiple context-specific graphs capturing spatial proximity, gene expression similarity, and tissue domain structure, and learns disentangled embeddings for each. These are fused using an attention-inspired strategy to yield a unified, biologically meaningful representation. A community-aware min-cut loss improves robustness over contrastive learning, particularly in sparse ST data. SemanticST supports mini-batch training, making it the first graph neural network scalable to large-scale datasets such as Xenium (500,000 cells). Benchmarking across four platforms (Visium, Slide-seq, Stereo-seq, Xenium) and multiple human and mouse tissues shows consistent 20 percentage gains in ARI, NMI, and trajectory fidelity over DeepST, GraphST, and IRIS. In re-analysis of breast cancer Xenium data, SemanticST revealed rare and clinically significant niches, including triple receptor-positive clusters, spatially distinct DCIS-to-IDC transition zones, and FOXC2 tumour-associated myoepithelial cells, suggesting non-canonical EMT programs with stem-like features. SemanticST thus provides a scalable, interpretable, and biologically grounded framework for spatial transcriptomics analysis, enabling robust discovery across tissue types and diseases, and paving the way for spatially resolved tissue atlases and next-generation precision medicine.
With the popularity of social media, an increasing number of users are joining group activities on online social platforms. This elicits the requirement of group identification (GI), which is to recommend groups to users. We reveal that users are influenced by both group-level and item-level interests, and these dual-level interests have a collaborative evolution relationship: joining a group expands the user's item interests, further prompting the user to join new groups. Ultimately, the two interests tend to align dynamically. However, existing GI methods fail to fully model this collaborative evolution relationship, ignoring the enhancement of group-level interests on item-level interests, and suffering from false-negative samples when aligning cross-level interests. In order to fully model the collaborative evolution relationship between dual-level user interests, we propose CI4GI, a Collaborative Interest-aware model for Group Identification. Specifically, we design an interest enhancement strategy that identifies additional interests of users from the items interacted with by the groups they have joined as a supplement to item-level interests. In addition, we adopt the distance between interest distributions of two users to optimize the identification of negative samples for a user, mitigating the interference of false-negative samples during cross-level interests alignment. The results of experiments on three real-world datasets demonstrate that CI4GI significantly outperforms state-of-the-art models.
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.
Deep learning on graphs has shown remarkable success across numerous applications, including social networks, bio-physics, traffic networks, and recommendation systems. Regardless of their successes, current methods frequently depend on the assumption that training and testing data share the same distribution, a condition rarely met in real-world scenarios. While graph-transformer (GT) backbones have recently outperformed traditional message-passing neural networks (MPNNs) in multiple in-distribution (ID) benchmarks, their effectiveness under distribution shifts remains largely unexplored. In this work, we address the challenge of out-of-distribution (OOD) generalization for graph neural networks, with a special focus on the impact of backbone architecture. We systematically evaluate GT and hybrid backbones in OOD settings and compare them to MPNNs. To do so, we adapt several leading domain generalization (DG) algorithms to work with GTs and assess their performance on a benchmark designed to test a variety of distribution shifts. Our results reveal that GT and hybrid GT-MPNN backbones consistently demonstrate stronger generalization ability compared to MPNNs, even without specialized DG algorithms. Additionally, we propose a novel post-training analysis approach that compares the clustering structure of the entire ID and OOD test datasets, specifically examining domain alignment and class separation. Demonstrating its model-agnostic design, this approach not only provided meaningful insights into GT and MPNN backbones. It also shows promise for broader applicability to DG problems beyond graph learning, offering a deeper perspective on generalization abilities that goes beyond standard accuracy metrics. Together, our findings highlight the promise of graph-transformers for robust, real-world graph learning and set a new direction for future research in OOD generalization.
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.
Operations in disaster response, search \& rescue, and military missions that involve multiple agents demand automated processes to support the planning of the courses of action (COA). Moreover, traverse-affecting changes in the environment (rain, snow, blockades, etc.) may impact the expected performance of a COA, making it desirable to have a pool of COAs that are diverse in task distributions across agents. Further, variations in agent capabilities, which could be human crews and/or autonomous systems, present practical opportunities and computational challenges to the planning process. This paper presents a new theoretical formulation and computational framework to generate such diverse pools of COAs for operations with soft variations in agent-task compatibility. Key to the problem formulation is a graph abstraction of the task space and the pool of COAs itself to quantify its diversity. Formulating the COAs as a centralized multi-robot task allocation problem, a genetic algorithm is used for (order-ignoring) allocations of tasks to each agent that jointly maximize diversity within the COA pool and overall compatibility of the agent-task mappings. A graph neural network is trained using a policy gradient approach to then perform single agent task sequencing in each COA, which maximizes completion rates adaptive to task features. Our tests of the COA generation process in a simulated environment demonstrate significant performance gain over a random walk baseline, small optimality gap in task sequencing, and execution time of about 50 minutes to plan up to 20 COAs for 5 agent/100 task operations.
Effective decision-making on networks often relies on learning from graph-structured data, where Graph Neural Networks (GNNs) play a central role, but they take efforts to configure and tune. In this demo, we propose LLMNet, showing how to design GNN automated through Large Language Models. Our system develops a set of agents that construct graph-related knowlege bases and then leverages Retrieval-Augmented Generation (RAG) to support automated configuration and refinement of GNN models through a knowledge-guided evolution process. These agents, equipped with specialized knowledge bases, extract insights into tasks and graph structures by interacting with the knowledge bases. Empirical results show LLMNet excels in twelve datasets across three graph learning tasks, validating its effectiveness of GNN model designing.
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.