Daily Papers

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However, most existing methods consider molecular generation for protein pockets independently while neglecting the underlying connections such as subpocket-level similarities. Subpockets are the local protein environments of ligand fragments and pockets with similar subpockets may bind the same molecular fragment (motif) even though their overall structures are different. Therefore, the trained models can hardly generalize to unseen protein pockets in real-world applications. In this paper, we propose a novel method DrugGPS for generalizable structure-based drug design. With the biochemical priors, we propose to learn subpocket prototypes and construct a global interaction graph to model the interactions between subpocket prototypes and molecular motifs. Moreover, a hierarchical graph transformer encoder and motif-based 3D molecule generation scheme are used to improve the model's performance. The experimental results show that our model consistently outperforms baselines in generating realistic drug candidates with high affinities in challenging out-of-distribution settings.

In this work, we seek new insights into the underlying challenges of the Scene Graph Generation (SGG) task. Quantitative and qualitative analysis of the Visual Genome dataset implies -- 1) Ambiguity: even if inter-object relationship contains the same object (or predicate), they may not be visually or semantically similar, 2) Asymmetry: despite the nature of the relationship that embodied the direction, it was not well addressed in previous studies, and 3) Higher-order contexts: leveraging the identities of certain graph elements can help to generate accurate scene graphs. Motivated by the analysis, we design a novel SGG framework, Local-to-Global Interaction Networks (LOGIN). Locally, interactions extract the essence between three instances of subject, object, and background, while baking direction awareness into the network by explicitly constraining the input order of subject and object. Globally, interactions encode the contexts between every graph component (i.e., nodes and edges). Finally, Attract & Repel loss is utilized to fine-tune the distribution of predicate embeddings. By design, our framework enables predicting the scene graph in a bottom-up manner, leveraging the possible complementariness. To quantify how much LOGIN is aware of relational direction, a new diagnostic task called Bidirectional Relationship Classification (BRC) is also proposed. Experimental results demonstrate that LOGIN can successfully distinguish relational direction than existing methods (in BRC task), while showing state-of-the-art results on the Visual Genome benchmark (in SGG task).

Recent studies on Graph Convolutional Networks (GCNs) reveal that the initial node representations (i.e., the node representations before the first-time graph convolution) largely affect the final model performance. However, when learning the initial representation for a node, most existing work linearly combines the embeddings of node features, without considering the interactions among the features (or feature embeddings). We argue that when the node features are categorical, e.g., in many real-world applications like user profiling and recommender system, feature interactions usually carry important signals for predictive analytics. Ignoring them will result in suboptimal initial node representation and thus weaken the effectiveness of the follow-up graph convolution. In this paper, we propose a new GCN model named CatGCN, which is tailored for graph learning when the node features are categorical. Specifically, we integrate two ways of explicit interaction modeling into the learning of initial node representation, i.e., local interaction modeling on each pair of node features and global interaction modeling on an artificial feature graph. We then refine the enhanced initial node representations with the neighborhood aggregation-based graph convolution. We train CatGCN in an end-to-end fashion and demonstrate it on semi-supervised node classification. Extensive experiments on three tasks of user profiling (the prediction of user age, city, and purchase level) from Tencent and Alibaba datasets validate the effectiveness of CatGCN, especially the positive effect of performing feature interaction modeling before graph convolution.

Much progress has been made recently on text classification with methods based on neural networks. In particular, models using attention mechanism such as BERT have shown to have the capability of capturing the contextual information within a sentence or document. However, their ability of capturing the global information about the vocabulary of a language is more limited. This latter is the strength of Graph Convolutional Networks (GCN). In this paper, we propose VGCN-BERT model which combines the capability of BERT with a Vocabulary Graph Convolutional Network (VGCN). Local information and global information interact through different layers of BERT, allowing them to influence mutually and to build together a final representation for classification. In our experiments on several text classification datasets, our approach outperforms BERT and GCN alone, and achieve higher effectiveness than that reported in previous studies.

Hyper-relational knowledge graphs (HKGs) extend standard knowledge graphs by associating attribute-value qualifiers to triples, which effectively represent additional fine-grained information about its associated triple. Hyper-relational knowledge graph completion (HKGC) aims at inferring unknown triples while considering its qualifiers. Most existing approaches to HKGC exploit a global-level graph structure to encode hyper-relational knowledge into the graph convolution message passing process. However, the addition of multi-hop information might bring noise into the triple prediction process. To address this problem, we propose HyperFormer, a model that considers local-level sequential information, which encodes the content of the entities, relations and qualifiers of a triple. More precisely, HyperFormer is composed of three different modules: an entity neighbor aggregator module allowing to integrate the information of the neighbors of an entity to capture different perspectives of it; a relation qualifier aggregator module to integrate hyper-relational knowledge into the corresponding relation to refine the representation of relational content; a convolution-based bidirectional interaction module based on a convolutional operation, capturing pairwise bidirectional interactions of entity-relation, entity-qualifier, and relation-qualifier. realize the depth perception of the content related to the current statement. Furthermore, we introduce a Mixture-of-Experts strategy into the feed-forward layers of HyperFormer to strengthen its representation capabilities while reducing the amount of model parameters and computation. Extensive experiments on three well-known datasets with four different conditions demonstrate HyperFormer's effectiveness. Datasets and code are available at https://github.com/zhiweihu1103/HKGC-HyperFormer.

Naturally controllable human-scene interaction (HSI) generation has an important role in various fields, such as VR/AR content creation and human-centered AI. However, existing methods are unnatural and unintuitive in their controllability, which heavily limits their application in practice. Therefore, we focus on a challenging task of naturally and controllably generating realistic and diverse HSIs from textual descriptions. From human cognition, the ideal generative model should correctly reason about spatial relationships and interactive actions. To that end, we propose Narrator, a novel relationship reasoning-based generative approach using a conditional variation autoencoder for naturally controllable generation given a 3D scene and a textual description. Also, we model global and local spatial relationships in a 3D scene and a textual description respectively based on the scene graph, and introduce a partlevel action mechanism to represent interactions as atomic body part states. In particular, benefiting from our relationship reasoning, we further propose a simple yet effective multi-human generation strategy, which is the first exploration for controllable multi-human scene interaction generation. Our extensive experiments and perceptual studies show that Narrator can controllably generate diverse interactions and significantly outperform existing works. The code and dataset will be available for research purposes.

Recent advances in learning multi-modal representation have witnessed the success in biomedical domains. While established techniques enable handling multi-modal information, the challenges are posed when extended to various clinical modalities and practical modalitymissing setting due to the inherent modality gaps. To tackle these, we propose an innovative Modality-prompted Heterogeneous Graph for Omnimodal Learning (GTP-4o), which embeds the numerous disparate clinical modalities into a unified representation, completes the deficient embedding of missing modality and reformulates the cross-modal learning with a graph-based aggregation. Specially, we establish a heterogeneous graph embedding to explicitly capture the diverse semantic properties on both the modality-specific features (nodes) and the cross-modal relations (edges). Then, we design a modality-prompted completion that enables completing the inadequate graph representation of missing modality through a graph prompting mechanism, which generates hallucination graphic topologies to steer the missing embedding towards the intact representation. Through the completed graph, we meticulously develop a knowledge-guided hierarchical cross-modal aggregation consisting of a global meta-path neighbouring to uncover the potential heterogeneous neighbors along the pathways driven by domain knowledge, and a local multi-relation aggregation module for the comprehensive cross-modal interaction across various heterogeneous relations. We assess the efficacy of our methodology on rigorous benchmarking experiments against prior state-of-the-arts. In a nutshell, GTP-4o presents an initial foray into the intriguing realm of embedding, relating and perceiving the heterogeneous patterns from various clinical modalities holistically via a graph theory. Project page: https://gtp-4-o.github.io/.

Human pose forecasting garners attention for its diverse applications. However, challenges in modeling the multi-modal nature of human motion and intricate interactions among agents persist, particularly with longer timescales and more agents. In this paper, we propose an interaction-aware trajectory-conditioned long-term multi-agent human pose forecasting model, utilizing a coarse-to-fine prediction approach: multi-modal global trajectories are initially forecasted, followed by respective local pose forecasts conditioned on each mode. In doing so, our Trajectory2Pose model introduces a graph-based agent-wise interaction module for a reciprocal forecast of local motion-conditioned global trajectory and trajectory-conditioned local pose. Our model effectively handles the multi-modality of human motion and the complexity of long-term multi-agent interactions, improving performance in complex environments. Furthermore, we address the lack of long-term (6s+) multi-agent (5+) datasets by constructing a new dataset from real-world images and 2D annotations, enabling a comprehensive evaluation of our proposed model. State-of-the-art prediction performance on both complex and simpler datasets confirms the generalized effectiveness of our method. The code is available at https://github.com/Jaewoo97/T2P.

Multimodal recommendation systems are increasingly becoming foundational technologies for e-commerce and content platforms, enabling personalized services by jointly modeling users' historical behaviors and the multimodal features of items (e.g., visual and textual). However, most existing methods rely on either static fusion strategies or graph-based local interaction modeling, facing two critical limitations: (1) insufficient ability to model fine-grained cross-modal associations, leading to suboptimal fusion quality; and (2) a lack of global distribution-level consistency, causing representational bias. To address these, we propose MambaRec, a novel framework that integrates local feature alignment and global distribution regularization via attention-guided learning. At its core, we introduce the Dilated Refinement Attention Module (DREAM), which uses multi-scale dilated convolutions with channel-wise and spatial attention to align fine-grained semantic patterns between visual and textual modalities. This module captures hierarchical relationships and context-aware associations, improving cross-modal semantic modeling. Additionally, we apply Maximum Mean Discrepancy (MMD) and contrastive loss functions to constrain global modality alignment, enhancing semantic consistency. This dual regularization reduces mode-specific deviations and boosts robustness. To improve scalability, MambaRec employs a dimensionality reduction strategy to lower the computational cost of high-dimensional multimodal features. Extensive experiments on real-world e-commerce datasets show that MambaRec outperforms existing methods in fusion quality, generalization, and efficiency. Our code has been made publicly available at https://github.com/rkl71/MambaRec.

Long-range dependencies are critical for effective graph representation learning, yet most existing datasets focus on small graphs tailored to inductive tasks, offering limited insight into long-range interactions. Current evaluations primarily compare models employing global attention (e.g., graph transformers) with those using local neighborhood aggregation (e.g., message-passing neural networks) without a direct measurement of long-range dependency. In this work, we introduce City-Networks, a novel large-scale transductive learning dataset derived from real-world city roads. This dataset features graphs with over 10^5 nodes and significantly larger diameters than those in existing benchmarks, naturally embodying long-range information. We annotate the graphs using an eccentricity-based approach, ensuring that the classification task inherently requires information from distant nodes. Furthermore, we propose a model-agnostic measurement based on the Jacobians of neighbors from distant hops, offering a principled quantification of long-range dependencies. Finally, we provide theoretical justifications for both our dataset design and the proposed measurement - particularly by focusing on over-smoothing and influence score dilution - which establishes a robust foundation for further exploration of long-range interactions in graph neural networks.

Large language models (LLMs) have shown promise in simulating human-like social behaviors. Social graphs provide high-quality supervision signals that encode both local interactions and global network structure, yet they remain underutilized for LLM training. To address this gap, we propose Graphia, the first general LLM-based social graph simulation framework that leverages graph data as supervision for LLM post-training via reinforcement learning. With GNN-based structural rewards, Graphia trains specialized agents to predict whom to interact with (destination selection) and how to interact (edge generation), followed by designed graph generation pipelines. We evaluate Graphia under two settings: Transductive Dynamic Graph Generation (TDGG), a micro-level task with our proposed node-wise interaction alignment metrics; and Inductive Dynamic Graph Generation (IDGG), a macro-level task with our proposed metrics for aligning emergent network properties. On three real-world networks, Graphia improves micro-level alignment by 6.1% in the composite destination selection score, 12% in edge classification accuracy, and 27.9% in edge content BERTScore over the strongest baseline. For macro-level alignment, it achieves 41.11% higher structural similarity and 32.98% better replication of social phenomena such as power laws and echo chambers. Graphia also supports counterfactual simulation, generating plausible behavioral shifts under platform incentives. Our results show that social graphs can serve as high-quality supervision signals for LLM post-training, closing the gap between agent behaviors and network dynamics for LLM-based simulation. Code is available at https://github.com/Ji-Cather/Graphia.git.

Understanding the various properties of glycans with machine learning has shown some preliminary promise. However, previous methods mainly focused on modeling the backbone structure of glycans as graphs of monosaccharides (i.e., sugar units), while they neglected the atomic structures underlying each monosaccharide, which are actually important indicators of glycan properties. We fill this blank by introducing the GlycanAA model for All-Atom-wise Glycan modeling. GlycanAA models a glycan as a heterogeneous graph with monosaccharide nodes representing its global backbone structure and atom nodes representing its local atomic-level structures. Based on such a graph, GlycanAA performs hierarchical message passing to capture from local atomic-level interactions to global monosaccharide-level interactions. To further enhance model capability, we pre-train GlycanAA on a high-quality unlabeled glycan dataset, deriving the PreGlycanAA model. We design a multi-scale mask prediction algorithm to endow the model about different levels of dependencies in a glycan. Extensive benchmark results show the superiority of GlycanAA over existing glycan encoders and verify the further improvements achieved by PreGlycanAA. We maintain all resources at https://github.com/kasawa1234/GlycanAA

Modelling interactions is critical in learning complex dynamical systems, namely systems of interacting objects with highly non-linear and time-dependent behaviour. A large class of such systems can be formalized as geometric graphs, i.e., graphs with nodes positioned in the Euclidean space given an arbitrarily chosen global coordinate system, for instance vehicles in a traffic scene. Notwithstanding the arbitrary global coordinate system, the governing dynamics of the respective dynamical systems are invariant to rotations and translations, also known as Galilean invariance. As ignoring these invariances leads to worse generalization, in this work we propose local coordinate frames per node-object to induce roto-translation invariance to the geometric graph of the interacting dynamical system. Further, the local coordinate frames allow for a natural definition of anisotropic filtering in graph neural networks. Experiments in traffic scenes, 3D motion capture, and colliding particles demonstrate that the proposed approach comfortably outperforms the recent state-of-the-art.

Graphs can be used to represent and reason about systems and a variety of metrics have been devised to quantify their global characteristics. However, little is currently known about how to construct a graph or improve an existing one given a target objective. In this work, we formulate the construction of a graph as a decision-making process in which a central agent creates topologies by trial and error and receives rewards proportional to the value of the target objective. By means of this conceptual framework, we propose an algorithm based on reinforcement learning and graph neural networks to learn graph construction and improvement strategies. Our core case study focuses on robustness to failures and attacks, a property relevant for the infrastructure and communication networks that power modern society. Experiments on synthetic and real-world graphs show that this approach can outperform existing methods while being cheaper to evaluate. It also allows generalization to out-of-sample graphs, as well as to larger out-of-distribution graphs in some cases. The approach is applicable to the optimization of other global structural properties of graphs.

Emotional support conversation aims at reducing the emotional distress of the help-seeker, which is a new and challenging task. It requires the system to explore the cause of help-seeker's emotional distress and understand their psychological intention to provide supportive responses. However, existing methods mainly focus on the sequential contextual information, ignoring the hierarchical relationships with the global cause and local psychological intention behind conversations, thus leads to a weak ability of emotional support. In this paper, we propose a Global-to-Local Hierarchical Graph Network to capture the multi-source information (global cause, local intentions and dialog history) and model hierarchical relationships between them, which consists of a multi-source encoder, a hierarchical graph reasoner, and a global-guide decoder. Furthermore, a novel training objective is designed to monitor semantic information of the global cause. Experimental results on the emotional support conversation dataset, ESConv, confirm that the proposed GLHG has achieved the state-of-the-art performance on the automatic and human evaluations. The code will be released in here \small{~https://github.com/pengwei-iie/GLHG}.

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by https://github.com/WxxShirley/Awesome-Graph-Prompt, and https://github.com/sheldonresearch/ProG, respectively.

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

The abundance of intestinal flora is closely related to human diseases, but diseases are not caused by a single gut microbe. Instead, they result from the complex interplay of numerous microbial entities. This intricate and implicit connection among gut microbes poses a significant challenge for disease prediction using abundance information from OTU data. Recently, several methods have shown potential in predicting corresponding diseases. However, these methods fail to learn the inner association among gut microbes from different hosts, leading to unsatisfactory performance. In this paper, we present a novel architecture, Unsupervised Multi-graph Merge Adversarial Network (UMMAN). UMMAN can obtain the embeddings of nodes in the Multi-Graph in an unsupervised scenario, so that it helps learn the multiplex association. Our method is the first to combine Graph Neural Network with the task of intestinal flora disease prediction. We employ complex relation-types to construct the Original-Graph and disrupt the relationships among nodes to generate corresponding Shuffled-Graph. We introduce the Node Feature Global Integration (NFGI) module to represent the global features of the graph. Furthermore, we design a joint loss comprising adversarial loss and hybrid attention loss to ensure that the real graph embedding aligns closely with the Original-Graph and diverges from the Shuffled-Graph. Comprehensive experiments on five classical OTU gut microbiome datasets demonstrate the effectiveness and stability of our method. (We will release our code soon.)

Despite the recent successes of vanilla Graph Neural Networks (GNNs) on many tasks, their foundation on pairwise interaction networks inherently limits their capacity to discern latent higher-order interactions in complex systems. To bridge this capability gap, we propose a novel approach exploiting the rich mathematical theory of simplicial complexes (SCs) - a robust tool for modeling higher-order interactions. Current SC-based GNNs are burdened by high complexity and rigidity, and quantifying higher-order interaction strengths remains challenging. Innovatively, we present a higher-order Flower-Petals (FP) model, incorporating FP Laplacians into SCs. Further, we introduce a Higher-order Graph Convolutional Network (HiGCN) grounded in FP Laplacians, capable of discerning intrinsic features across varying topological scales. By employing learnable graph filters, a parameter group within each FP Laplacian domain, we can identify diverse patterns where the filters' weights serve as a quantifiable measure of higher-order interaction strengths. The theoretical underpinnings of HiGCN's advanced expressiveness are rigorously demonstrated. Additionally, our empirical investigations reveal that the proposed model accomplishes state-of-the-art (SOTA) performance on a range of graph tasks and provides a scalable and flexible solution to explore higher-order interactions in graphs.

Large Language Models~(LLMs) have demonstrated capabilities across various applications but face challenges such as hallucination, limited reasoning abilities, and factual inconsistencies, especially when tackling complex, domain-specific tasks like question answering~(QA). While Knowledge Graphs~(KGs) have been shown to help mitigate these issues, research on the integration of LLMs with background KGs remains limited. In particular, user accessibility and the flexibility of the underlying KG have not been thoroughly explored. We introduce AGENTiGraph (Adaptive Generative ENgine for Task-based Interaction and Graphical Representation), a platform for knowledge management through natural language interaction. It integrates knowledge extraction, integration, and real-time visualization. AGENTiGraph employs a multi-agent architecture to dynamically interpret user intents, manage tasks, and integrate new knowledge, ensuring adaptability to evolving user requirements and data contexts. Our approach demonstrates superior performance in knowledge graph interactions, particularly for complex domain-specific tasks. Experimental results on a dataset of 3,500 test cases show AGENTiGraph significantly outperforms state-of-the-art zero-shot baselines, achieving 95.12\% accuracy in task classification and 90.45\% success rate in task execution. User studies corroborate its effectiveness in real-world scenarios. To showcase versatility, we extended AGENTiGraph to legislation and healthcare domains, constructing specialized KGs capable of answering complex queries in legal and medical contexts.

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Graphs have often been used to answer questions about the interaction between real-world entities by taking advantage of their capacity to represent complex topologies. Complex networks are known to be graphs that capture such non-trivial topologies; they are able to represent human phenomena such as epidemic processes, the dynamics of populations, and the urbanization of cities. The investigation of complex networks has been extrapolated to many fields of science, with particular emphasis on computing techniques, including artificial intelligence. In such a case, the analysis of the interaction between entities of interest is transposed to the internal learning of algorithms, a paradigm whose investigation is able to expand the state of the art in Computer Science. By exploring this paradigm, this thesis puts together complex networks and machine learning techniques to improve the understanding of the human phenomena observed in pandemics, pendular migration, and street networks. Accordingly, we contribute with: (i) a new neural network architecture capable of modeling dynamic processes observed in spatial and temporal data with applications in epidemics propagation, weather forecasting, and patient monitoring in intensive care units; (ii) a machine-learning methodology for analyzing and predicting links in the scope of human mobility between all the cities of Brazil; and, (iii) techniques for identifying inconsistencies in the urban planning of cities while tracking the most influential vertices, with applications over Brazilian and worldwide cities. We obtained results sustained by sound evidence of advances to the state of the art in artificial intelligence, rigorous formalisms, and ample experimentation. Our findings rely upon real-world applications in a range of domains, demonstrating the applicability of our methodologies.

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

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 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, 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. In contrast, 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.

Various human-designed prompt engineering techniques have been proposed to improve problem solvers based on Large Language Models (LLMs), yielding many disparate code bases. We unify these approaches by describing LLM-based agents as computational graphs. The nodes implement functions to process multimodal data or query LLMs, and the edges describe the information flow between operations. Graphs can be recursively combined into larger composite graphs representing hierarchies of inter-agent collaboration (where edges connect operations of different agents). Our novel automatic graph optimizers (1) refine node-level LLM prompts (node optimization) and (2) improve agent orchestration by changing graph connectivity (edge optimization). Experiments demonstrate that our framework can be used to efficiently develop, integrate, and automatically improve various LLM agents. The code can be found at https://github.com/metauto-ai/gptswarm.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Hypergraphs offer a powerful framework for modeling higher-order interactions that traditional pairwise graphs cannot fully capture. However, practical constraints often lead to their simplification into projected graphs, resulting in substantial information loss and ambiguity in representing higher-order relationships. In this work, we propose MARIOH, a supervised approach for reconstructing the original hypergraph from its projected graph by leveraging edge multiplicity. To overcome the difficulties posed by the large search space, MARIOH integrates several key ideas: (a) identifying provable size-2 hyperedges, which reduces the candidate search space, (b) predicting the likelihood of candidates being hyperedges by utilizing both structural and multiplicity-related features, and (c) not only targeting promising hyperedge candidates but also examining less confident ones to explore alternative possibilities. Together, these ideas enable MARIOH to efficiently and effectively explore the search space. In our experiments using 10 real-world datasets, MARIOH achieves up to 74.51% higher reconstruction accuracy compared to state-of-the-art methods.

Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.

Rationale discovery is defined as finding a subset of the input data that maximally supports the prediction of downstream tasks. In graph machine learning context, graph rationale is defined to locate the critical subgraph in the given graph topology, which fundamentally determines the prediction results. In contrast to the rationale subgraph, the remaining subgraph is named the environment subgraph. Graph rationalization can enhance the model performance as the mapping between the graph rationale and prediction label is viewed as invariant, by assumption. To ensure the discriminative power of the extracted rationale subgraphs, a key technique named "intervention" is applied. The core idea of intervention is that given any changing environment subgraphs, the semantics from the rationale subgraph is invariant, which guarantees the correct prediction result. However, most, if not all, of the existing rationalization works on graph data develop their intervention strategies on the graph level, which is coarse-grained. In this paper, we propose well-tailored intervention strategies on graph data. Our idea is driven by the development of Transformer models, whose self-attention module provides rich interactions between input nodes. Based on the self-attention module, our proposed invariant graph Transformer (IGT) can achieve fine-grained, more specifically, node-level and virtual node-level intervention. Our comprehensive experiments involve 7 real-world datasets, and the proposed IGT shows significant performance advantages compared to 13 baseline methods.

In this study, we propose a novel graph-based approach to model, analyze and comprehend user interactions within a social media platform based on post-comment relationship. We construct a user interaction graph from social media data and analyze it to gain insights into community dynamics, user behavior, and content preferences. Our investigation reveals that while 56.05% of the active users are strongly connected within the community, only 0.8% of them significantly contribute to its dynamics. Moreover, we observe temporal variations in community activity, with certain periods experiencing heightened engagement. Additionally, our findings highlight a correlation between user activity and popularity showing that more active users are generally more popular. Alongside these, a preference for positive and informative content is also observed where 82.41% users preferred positive and informative content. Overall, our study provides a comprehensive framework for understanding and managing online communities, leveraging graph-based techniques to gain valuable insights into user behavior and community dynamics.

Existing commonsense knowledge bases often organize tuples in an isolated manner, which is deficient for commonsense conversational models to plan the next steps. To fill the gap, we curate a large-scale multi-turn human-written conversation corpus, and create the first Chinese commonsense conversation knowledge graph which incorporates both social commonsense knowledge and dialog flow information. To show the potential of our graph, we develop a graph-conversation matching approach, and benchmark two graph-grounded conversational tasks.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

Real-world networks, with their evolving relations, are best captured as temporal graphs. However, existing software libraries are largely designed for static graphs where the dynamic nature of temporal graphs is ignored. Bridging this gap, we introduce TGX, a Python package specially designed for analysis of temporal networks that encompasses an automated pipeline for data loading, data processing, and analysis of evolving graphs. TGX provides access to eleven built-in datasets and eight external Temporal Graph Benchmark (TGB) datasets as well as any novel datasets in the .csv format. Beyond data loading, TGX facilitates data processing functionalities such as discretization of temporal graphs and node subsampling to accelerate working with larger datasets. For comprehensive investigation, TGX offers network analysis by providing a diverse set of measures, including average node degree and the evolving number of nodes and edges per timestamp. Additionally, the package consolidates meaningful visualization plots indicating the evolution of temporal patterns, such as Temporal Edge Appearance (TEA) and Temporal Edge Trafficc (TET) plots. The TGX package is a robust tool for examining the features of temporal graphs and can be used in various areas like studying social networks, citation networks, and tracking user interactions. We plan to continuously support and update TGX based on community feedback. TGX is publicly available on: https://github.com/ComplexData-MILA/TGX.

Graphs are widely used for modeling relational data in real-world scenarios, such as social networks and urban computing. Existing LLM-based graph analysis approaches either integrate graph neural networks (GNNs) for specific machine learning tasks, limiting their transferability, or rely solely on LLMs' internal reasoning ability, resulting in suboptimal performance. To address these limitations, we take advantage of recent advances in LLM-based agents, which have shown capabilities of utilizing external knowledge or tools for problem solving. By simulating human problem-solving strategies such as analogy and collaboration, we propose a multi-agent system based on LLMs named GraphTeam, for graph analysis. GraphTeam consists of five LLM-based agents from three modules, and the agents with different specialities can collaborate with each other to address complex problems. Specifically, (1) input-output normalization module: the question agent extracts and refines four key arguments from the original question, facilitating the problem understanding, and the answer agent organizes the results to meet the output requirement; (2) external knowledge retrieval module: we first build a knowledge base consisting of relevant documentation and experience information, and then the search agent retrieves the most relevant entries for each question. (3) problem-solving module: given the retrieved information from search agent, the coding agent uses established algorithms via programming to generate solutions, and in case the coding agent does not work, the reasoning agent will directly compute the results without programming. Extensive experiments on six graph analysis benchmarks demonstrate that GraphTeam achieves state-of-the-art performance with an average 25.85% improvement over the best baseline in terms of accuracy. The code and data are available at https://github.com/BUPT-GAMMA/GraphTeam.

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

In this paper, we aim to develop a large language model (LLM) with the reasoning ability on complex graph data. Currently, LLMs have achieved very impressive performance on various natural language learning tasks, extensions of which have also been applied to study the vision tasks with multi-modal data. However, when it comes to the graph learning tasks, existing LLMs present very serious flaws due to their several inherited weaknesses in performing {multi-step logic reasoning}, {precise mathematical calculation} and {perception about the spatial and temporal factors}. To address such challenges, in this paper, we will investigate the principles, methodologies and algorithms to empower existing LLMs with graph reasoning ability, which will have tremendous impacts on the current research of both LLMs and graph learning. Inspired by the latest ChatGPT and Toolformer models, we propose the Graph-ToolFormer (Graph Reasoning oriented Toolformer) framework to teach LLMs themselves with prompts augmented by ChatGPT to use external graph reasoning API tools. Specifically, we will investigate to teach Graph-ToolFormer to handle various graph data reasoning tasks in this paper, including both (1) very basic graph data loading and graph property reasoning tasks, ranging from simple graph order and size to the graph diameter and periphery, and (2) more advanced reasoning tasks on real-world graph data, such as bibliographic networks, protein molecules, sequential recommender systems, social networks and knowledge graphs.

Hypergraphs are a powerful abstraction for representing higher-order interactions between entities of interest. To exploit these relationships in making downstream predictions, a variety of hypergraph neural network architectures have recently been proposed, in large part building upon precursors from the more traditional graph neural network (GNN) literature. Somewhat differently, in this paper we begin by presenting an expressive family of parameterized, hypergraph-regularized energy functions. We then demonstrate how minimizers of these energies effectively serve as node embeddings that, when paired with a parameterized classifier, can be trained end-to-end via a supervised bilevel optimization process. Later, we draw parallels between the implicit architecture of the predictive models emerging from the proposed bilevel hypergraph optimization, and existing GNN architectures in common use. Empirically, we demonstrate state-of-the-art results on various hypergraph node classification benchmarks. Code is available at https://github.com/yxzwang/PhenomNN.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

Graph-based collaborative filtering methods have prevailing performance for recommender systems since they can capture high-order information between users and items, in which the graphs are constructed from the observed user-item interactions that might miss links or contain spurious positive interactions in industrial scenarios. The Bayesian Graph Neural Network framework approaches this issue with generative models for the interaction graphs. The critical problem is to devise a proper family of graph generative models tailored to recommender systems. We propose an efficient generative model that jointly considers the preferences of users, the concurrence of items and some important graph structure information. Experiments on four popular benchmark datasets demonstrate the effectiveness of our proposed graph generative methods for recommender systems.

Graph Neural Networks operate through bottom-up message-passing, fundamentally differing from human visual perception, which intuitively captures global structures first. We investigate the underappreciated potential of vision models for graph understanding, finding they achieve performance comparable to GNNs on established benchmarks while exhibiting distinctly different learning patterns. These divergent behaviors, combined with limitations of existing benchmarks that conflate domain features with topological understanding, motivate our introduction of GraphAbstract. This benchmark evaluates models' ability to perceive global graph properties as humans do: recognizing organizational archetypes, detecting symmetry, sensing connectivity strength, and identifying critical elements. Our results reveal that vision models significantly outperform GNNs on tasks requiring holistic structural understanding and maintain generalizability across varying graph scales, while GNNs struggle with global pattern abstraction and degrade with increasing graph size. This work demonstrates that vision models possess remarkable yet underutilized capabilities for graph structural understanding, particularly for problems requiring global topological awareness and scale-invariant reasoning. These findings open new avenues to leverage this underappreciated potential for developing more effective graph foundation models for tasks dominated by holistic pattern recognition.

Graph Neural Networks (GNNs) that are based on the message passing (MP) paradigm generally exchange information between 1-hop neighbors to build node representations at each layer. In principle, such networks are not able to capture long-range interactions (LRI) that may be desired or necessary for learning a given task on graphs. Recently, there has been an increasing interest in development of Transformer-based methods for graphs that can consider full node connectivity beyond the original sparse structure, thus enabling the modeling of LRI. However, MP-GNNs that simply rely on 1-hop message passing often fare better in several existing graph benchmarks when combined with positional feature representations, among other innovations, hence limiting the perceived utility and ranking of Transformer-like architectures. Here, we present the Long Range Graph Benchmark (LRGB) with 5 graph learning datasets: PascalVOC-SP, COCO-SP, PCQM-Contact, Peptides-func and Peptides-struct that arguably require LRI reasoning to achieve strong performance in a given task. We benchmark both baseline GNNs and Graph Transformer networks to verify that the models which capture long-range dependencies perform significantly better on these tasks. Therefore, these datasets are suitable for benchmarking and exploration of MP-GNNs and Graph Transformer architectures that are intended to capture LRI.

Emotions are an inherent part of human interactions, and consequently, it is imperative to develop AI systems that understand and recognize human emotions. During a conversation involving various people, a person's emotions are influenced by the other speaker's utterances and their own emotional state over the utterances. In this paper, we propose COntextualized Graph Neural Network based Multimodal Emotion recognitioN (COGMEN) system that leverages local information (i.e., inter/intra dependency between speakers) and global information (context). The proposed model uses Graph Neural Network (GNN) based architecture to model the complex dependencies (local and global information) in a conversation. Our model gives state-of-the-art (SOTA) results on IEMOCAP and MOSEI datasets, and detailed ablation experiments show the importance of modeling information at both levels.

Many real-world systems exhibit temporal, dynamic behaviors, which are captured as time series of complex agent interactions. To perform temporal reasoning, current methods primarily encode temporal dynamics through simple sequence-based models. However, in general these models fail to efficiently capture the full spectrum of rich dynamics in the input, since the dynamics is not uniformly distributed. In particular, relevant information might be harder to extract and computing power is wasted for processing all individual timesteps, even if they contain no significant changes or no new information. Here we propose TimeGraphs, a novel approach that characterizes dynamic interactions as a hierarchical temporal graph, diverging from traditional sequential representations. Our approach models the interactions using a compact graph-based representation, enabling adaptive reasoning across diverse time scales. Adopting a self-supervised method, TimeGraphs constructs a multi-level event hierarchy from a temporal input, which is then used to efficiently reason about the unevenly distributed dynamics. This construction process is scalable and incremental to accommodate streaming data. We evaluate TimeGraphs on multiple datasets with complex, dynamic agent interactions, including a football simulator, the Resistance game, and the MOMA human activity dataset. The results demonstrate both robustness and efficiency of TimeGraphs on a range of temporal reasoning tasks. Our approach obtains state-of-the-art performance and leads to a performance increase of up to 12.2% on event prediction and recognition tasks over current approaches. Our experiments further demonstrate a wide array of capabilities including zero-shot generalization, robustness in case of data sparsity, and adaptability to streaming data flow.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined "LLMs-as-Consultants," which integrates LLMs with GNNs in an interactive manner. A framework named LOGIN (LLM Consulted GNN training) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of LOGIN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at https://github.com/QiaoYRan/LOGIN.

Prediction of protein-ligand (PL) binding affinity remains the key to drug discovery. Popular approaches in recent years involve graph neural networks (GNNs), which are used to learn the topology and geometry of PL complexes. However, GNNs are computationally heavy and have poor scalability to graph sizes. On the other hand, traditional machine learning (ML) approaches, such as gradient-boosted decision trees (GBDTs), are lightweight yet extremely efficient for tabular data. We propose to use PL interaction features along with PL graph-level features in GBDT. We show that this combination outperforms the existing solutions.

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the computational feasibility of the global attention mechanism is possible. The next goal is to scale up these architectures to handle very large graphs on the scale of millions or even billions of nodes. With large-scale graphs, global attention learning is proven impractical due to its quadratic complexity w.r.t. the number of nodes. On the other hand, neighborhood sampling techniques become essential to manage large graph sizes, yet finding the optimal trade-off between speed and accuracy with sampling techniques remains challenging. This work advances representation learning on single large-scale graphs with a focus on identifying model characteristics and critical design constraints for developing scalable graph transformer (GT) architectures. We argue such GT requires layers that can adeptly learn both local and global graph representations while swiftly sampling the graph topology. As such, a key innovation of this work lies in the creation of a fast neighborhood sampling technique coupled with a local attention mechanism that encompasses a 4-hop reception field, but achieved through just 2-hop operations. This local node embedding is then integrated with a global node embedding, acquired via another self-attention layer with an approximate global codebook, before finally sent through a downstream layer for node predictions. The proposed GT framework, named LargeGT, overcomes previous computational bottlenecks and is validated on three large-scale node classification benchmarks. We report a 3x speedup and 16.8% performance gain on ogbn-products and snap-patents, while we also scale LargeGT on ogbn-papers100M with a 5.9% performance improvement.

Graph Neural Networks (GNNs) have demonstrated superior performance on various graph learning tasks, including recommendation, where they leverage user-item collaborative filtering signals in graphs. However, theoretical formulations of their capability are scarce, despite their empirical effectiveness in state-of-the-art recommender models. Recently, research has explored the expressiveness of GNNs in general, demonstrating that message passing GNNs are at most as powerful as the Weisfeiler-Lehman test, and that GNNs combined with random node initialization are universal. Nevertheless, the concept of "expressiveness" for GNNs remains vaguely defined. Most existing works adopt the graph isomorphism test as the metric of expressiveness, but this graph-level task may not effectively assess a model's ability in recommendation, where the objective is to distinguish nodes of different closeness. In this paper, we provide a comprehensive theoretical analysis of the expressiveness of GNNs in recommendation, considering three levels of expressiveness metrics: graph isomorphism (graph-level), node automorphism (node-level), and topological closeness (link-level). We propose the topological closeness metric to evaluate GNNs' ability to capture the structural distance between nodes, which aligns closely with the objective of recommendation. To validate the effectiveness of this new metric in evaluating recommendation performance, we introduce a learning-less GNN algorithm that is optimal on the new metric and can be optimal on the node-level metric with suitable modification. We conduct extensive experiments comparing the proposed algorithm against various types of state-of-the-art GNN models to explore the explainability of the new metric in the recommendation task. For reproducibility, implementation codes are available at https://github.com/HKUDS/GTE.

While large-scale human motion capture datasets have advanced human motion generation, modeling and generating dynamic 3D human-object interactions (HOIs) remain challenging due to dataset limitations. Existing datasets often lack extensive, high-quality motion and annotation and exhibit artifacts such as contact penetration, floating, and incorrect hand motions. To address these issues, we introduce InterAct, a large-scale 3D HOI benchmark featuring dataset and methodological advancements. First, we consolidate and standardize 21.81 hours of HOI data from diverse sources, enriching it with detailed textual annotations. Second, we propose a unified optimization framework to enhance data quality by reducing artifacts and correcting hand motions. Leveraging the principle of contact invariance, we maintain human-object relationships while introducing motion variations, expanding the dataset to 30.70 hours. Third, we define six benchmarking tasks and develop a unified HOI generative modeling perspective, achieving state-of-the-art performance. Extensive experiments validate the utility of our dataset as a foundational resource for advancing 3D human-object interaction generation. To support continued research in this area, the dataset is publicly available at https://github.com/wzyabcas/InterAct, and will be actively maintained.

Graph learning has become indispensable for interpreting and harnessing relational data in diverse fields, ranging from recommendation systems to social network analysis. In this context, a variety of GNNs have emerged as promising methodologies for encoding the structural information of graphs. By effectively capturing the graph's underlying structure, these GNNs have shown great potential in enhancing performance in graph learning tasks, such as link prediction and node classification. However, despite their successes, a significant challenge persists: these advanced methods often face difficulties in generalizing to unseen graph data that significantly differs from the training instances. In this work, our aim is to advance the graph learning paradigm by developing a general graph foundation model. This model is designed to understand the complex topological patterns present in diverse graph data, enabling it to excel in zero-shot graph learning tasks across different downstream datasets. To achieve this goal, we address several key technical challenges in our OpenGraph model. Firstly, we propose a unified graph tokenizer to adapt our graph model to generalize well on unseen graph data, even when the underlying graph properties differ significantly from those encountered during training. Secondly, we develop a scalable graph transformer as the foundational encoder, which effectively captures node-wise dependencies within the global topological context. Thirdly, we introduce a data augmentation mechanism enhanced by a LLM to alleviate the limitations of data scarcity in real-world scenarios. Extensive experiments validate the effectiveness of our framework. By adapting our OpenGraph to new graph characteristics and comprehending the nuances of diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings and domains.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

Graph In-Context Learning, with the ability to adapt pre-trained graph models to novel and diverse downstream graphs without updating any parameters, has gained much attention in the community. The key to graph in-context learning is to perform downstream graphs conditioned on chosen prompt examples. Existing methods randomly select subgraphs or edges as prompts, leading to noisy graph prompts and inferior model performance. Additionally, due to the gap between pre-training and testing graphs, when the number of classes in the testing graphs is much greater than that in the training, the in-context learning ability will also significantly deteriorate. To tackle the aforementioned challenges, we develop a multi-stage adaptive prompt optimization method GraphPrompter, which optimizes the entire process of generating, selecting, and using graph prompts for better in-context learning capabilities. Firstly, Prompt Generator introduces a reconstruction layer to highlight the most informative edges and reduce irrelevant noise for graph prompt construction. Furthermore, in the selection stage, Prompt Selector employs the k-nearest neighbors algorithm and pre-trained selection layers to dynamically choose appropriate samples and minimize the influence of irrelevant prompts. Finally, we leverage a Prompt Augmenter with a cache replacement strategy to enhance the generalization capability of the pre-trained model on new datasets. Extensive experiments show that GraphPrompter effectively enhances the in-context learning ability of graph models. On average across all the settings, our approach surpasses the state-of-the-art baselines by over 8%. Our code is released at https://github.com/karin0018/GraphPrompter.

With the increase of data in day-to-day life, businesses and different stakeholders need to analyze the data for better predictions. Traditionally, relational data has been a source of various insights, but with the increase in computational power and the need to understand deeper relationships between entities, the need to design new techniques has arisen. For this graph data analysis has become an extraordinary tool for understanding the data, which reveals more realistic and flexible modelling of complex relationships. Recently, Graph Neural Networks (GNNs) have shown great promise in various applications, such as social network analysis, recommendation systems, drug discovery, and more. However, many adversarial attacks can happen over the data, whether during training (poisoning attack) or during testing (evasion attack), which can adversely manipulate the desired outcome from the GNN model. Therefore, it is crucial to make the GNNs robust to such attacks. The existing robustness methods are computationally demanding and perform poorly when the intensity of attack increases. This paper presents a computationally efficient framework, namely, pLapGNN, based on weighted p-Laplacian for making GNNs robust. Empirical evaluation on real datasets establishes the efficacy and efficiency of the proposed method.

Foundation models like ChatGPT and GPT-4 have revolutionized artificial intelligence, exhibiting remarkable abilities to generalize across a wide array of tasks and applications beyond their initial training objectives. However, graph learning has predominantly focused on single-graph models, tailored to specific tasks or datasets, lacking the ability to transfer learned knowledge to different domains. This limitation stems from the inherent complexity and diversity of graph structures, along with the different feature and label spaces specific to graph data. In this paper, we recognize text as an effective unifying medium and employ Text-Attributed Graphs (TAGs) to leverage this potential. We present our UniGraph framework, designed to learn a foundation model for TAGs, which is capable of generalizing to unseen graphs and tasks across diverse domains. Unlike single-graph models that use pre-computed node features of varying dimensions as input, our approach leverages textual features for unifying node representations, even for graphs such as molecular graphs that do not naturally have textual features. We propose a novel cascaded architecture of Language Models (LMs) and Graph Neural Networks (GNNs) as backbone networks. Additionally, we propose the first pre-training algorithm specifically designed for large-scale self-supervised learning on TAGs, based on Masked Graph Modeling. We introduce graph instruction tuning using Large Language Models (LLMs) to enable zero-shot prediction ability. Our comprehensive experiments across various graph learning tasks and domains demonstrate the model's effectiveness in self-supervised representation learning on unseen graphs, few-shot in-context transfer, and zero-shot transfer, even surpassing or matching the performance of GNNs that have undergone supervised training on target datasets.

This paper explores the advancements and applications of large-scale models in the medical field, with a particular focus on Medical Large Models (MedLMs). These models, encompassing Large Language Models (LLMs), Vision Models, 3D Large Models, and Multimodal Models, are revolutionizing healthcare by enhancing disease prediction, diagnostic assistance, personalized treatment planning, and drug discovery. The integration of graph neural networks in medical knowledge graphs and drug discovery highlights the potential of Large Graph Models (LGMs) in understanding complex biomedical relationships. The study also emphasizes the transformative role of Vision-Language Models (VLMs) and 3D Large Models in medical image analysis, anatomical modeling, and prosthetic design. Despite the challenges, these technologies are setting new benchmarks in medical innovation, improving diagnostic accuracy, and paving the way for personalized healthcare solutions. This paper aims to provide a comprehensive overview of the current state and future directions of large models in medicine, underscoring their significance in advancing global health.

This work addresses a new challenge of understanding human nonverbal interaction in social contexts. Nonverbal signals pervade virtually every communicative act. Our gestures, facial expressions, postures, gaze, even physical appearance all convey messages, without anything being said. Despite their critical role in social life, nonverbal signals receive very limited attention as compared to the linguistic counterparts, and existing solutions typically examine nonverbal cues in isolation. Our study marks the first systematic effort to enhance the interpretation of multifaceted nonverbal signals. First, we contribute a novel large-scale dataset, called NVI, which is meticulously annotated to include bounding boxes for humans and corresponding social groups, along with 22 atomic-level nonverbal behaviors under five broad interaction types. Second, we establish a new task NVI-DET for nonverbal interaction detection, which is formalized as identifying triplets in the form <individual, group, interaction> from images. Third, we propose a nonverbal interaction detection hypergraph (NVI-DEHR), a new approach that explicitly models high-order nonverbal interactions using hypergraphs. Central to the model is a dual multi-scale hypergraph that adeptly addresses individual-to-individual and group-to-group correlations across varying scales, facilitating interactional feature learning and eventually improving interaction prediction. Extensive experiments on NVI show that NVI-DEHR improves various baselines significantly in NVI-DET. It also exhibits leading performance on HOI-DET, confirming its versatility in supporting related tasks and strong generalization ability. We hope that our study will offer the community new avenues to explore nonverbal signals in more depth.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological information of a graph using persistent homology. TOGL can be easily integrated into any type of GNN and is strictly more expressive (in terms the Weisfeiler--Lehman graph isomorphism test) than message-passing GNNs. Augmenting GNNs with TOGL leads to improved predictive performance for graph and node classification tasks, both on synthetic data sets, which can be classified by humans using their topology but not by ordinary GNNs, and on real-world data.

We present a unified representation for actionable spatial perception: 3D Dynamic Scene Graphs. Scene graphs are directed graphs where nodes represent entities in the scene (e.g. objects, walls, rooms), and edges represent relations (e.g. inclusion, adjacency) among nodes. Dynamic scene graphs (DSGs) extend this notion to represent dynamic scenes with moving agents (e.g. humans, robots), and to include actionable information that supports planning and decision-making (e.g. spatio-temporal relations, topology at different levels of abstraction). Our second contribution is to provide the first fully automatic Spatial PerceptIon eNgine(SPIN) to build a DSG from visual-inertial data. We integrate state-of-the-art techniques for object and human detection and pose estimation, and we describe how to robustly infer object, robot, and human nodes in crowded scenes. To the best of our knowledge, this is the first paper that reconciles visual-inertial SLAM and dense human mesh tracking. Moreover, we provide algorithms to obtain hierarchical representations of indoor environments (e.g. places, structures, rooms) and their relations. Our third contribution is to demonstrate the proposed spatial perception engine in a photo-realistic Unity-based simulator, where we assess its robustness and expressiveness. Finally, we discuss the implications of our proposal on modern robotics applications. 3D Dynamic Scene Graphs can have a profound impact on planning and decision-making, human-robot interaction, long-term autonomy, and scene prediction. A video abstract is available at https://youtu.be/SWbofjhyPzI

Large Language Models (LLMs) have gained the ability to assimilate human knowledge and facilitate natural language interactions with both humans and other LLMs. However, despite their impressive achievements, LLMs have not made significant advancements in the realm of graph machine learning. This limitation arises because graphs encapsulate distinct relational data, making it challenging to transform them into natural language that LLMs understand. In this paper, we bridge this gap with a novel framework, GraphText, that translates graphs into natural language. GraphText derives a graph-syntax tree for each graph that encapsulates both the node attributes and inter-node relationships. Traversal of the tree yields a graph text sequence, which is then processed by an LLM to treat graph tasks as text generation tasks. Notably, GraphText offers multiple advantages. It introduces training-free graph reasoning: even without training on graph data, GraphText with ChatGPT can achieve on par with, or even surpassing, the performance of supervised-trained graph neural networks through in-context learning (ICL). Furthermore, GraphText paves the way for interactive graph reasoning, allowing both humans and LLMs to communicate with the model seamlessly using natural language. These capabilities underscore the vast, yet-to-be-explored potential of LLMs in the domain of graph machine learning.

The construction of Generalized Knowledge Graph (GKG), including knowledge graph, event knowledge graph and commonsense knowledge graph, is fundamental for various natural language processing tasks. Current studies typically construct these types of graph separately, overlooking holistic insights and potential unification that could be beneficial in computing resources and usage perspectives. However, a key challenge in developing a unified framework for GKG is obstacles arising from task-specific differences. In this study, we propose a unified framework for constructing generalized knowledge graphs to address this challenge. First, we collect data from 15 sub-tasks in 29 datasets across the three types of graphs, categorizing them into in-sample, counter-task, and out-of-distribution (OOD) data. Then, we propose a three-stage curriculum learning fine-tuning framework, by iteratively injecting knowledge from the three types of graphs into the Large Language Models. Extensive experiments show that our proposed model improves the construction of all three graph types across in-domain, OOD and counter-task data.

The concept of 3D scene graphs is increasingly recognized as a powerful semantic and hierarchical representation of the environment. Current approaches often address this at a coarse, object-level resolution. In contrast, our goal is to develop a representation that enables robots to directly interact with their environment by identifying both the location of functional interactive elements and how these can be used. To achieve this, we focus on detecting and storing objects at a finer resolution, focusing on affordance-relevant parts. The primary challenge lies in the scarcity of data that extends beyond instance-level detection and the inherent difficulty of capturing detailed object features using robotic sensors. We leverage currently available 3D resources to generate 2D data and train a detector, which is then used to augment the standard 3D scene graph generation pipeline. Through our experiments, we demonstrate that our approach achieves functional element segmentation comparable to state-of-the-art 3D models and that our augmentation enables task-driven affordance grounding with higher accuracy than the current solutions. See our project page at https://fungraph.github.io.

The rapidly growing number and variety of Large Language Models (LLMs) present significant challenges in efficiently selecting the appropriate LLM for a given query, especially considering the trade-offs between performance and computational cost. Current LLM selection methods often struggle to generalize across new LLMs and different tasks because of their limited ability to leverage contextual interactions among tasks, queries, and LLMs, as well as their dependence on a transductive learning framework. To address these shortcomings, we introduce a novel inductive graph framework, named as GraphRouter, which fully utilizes the contextual information among tasks, queries, and LLMs to enhance the LLM selection process. GraphRouter constructs a heterogeneous graph comprising task, query, and LLM nodes, with interactions represented as edges, which efficiently captures the contextual information between the query's requirements and the LLM's capabilities. Through an innovative edge prediction mechanism, GraphRouter is able to predict attributes (the effect and cost of LLM response) of potential edges, allowing for optimized recommendations that adapt to both existing and newly introduced LLMs without requiring retraining. Comprehensive experiments across three distinct effect-cost weight scenarios have shown that GraphRouter substantially surpasses existing routers, delivering a minimum performance improvement of 12.3%. In addition, it achieves enhanced generalization across new LLMs settings and supports diverse tasks with at least a 9.5% boost in effect and a significant reduction in computational demands. This work endeavors to apply a graph-based approach for the contextual and adaptive selection of LLMs, offering insights for real-world applications. Our codes for GraphRouter is released at https://github.com/ulab-uiuc/GraphRouter.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

A key requirement for graph neural networks is that they must process a graph in a way that does not depend on how the graph is described. Traditionally this has been taken to mean that a graph network must be equivariant to node permutations. Here we show that instead of equivariance, the more general concept of naturality is sufficient for a graph network to be well-defined, opening up a larger class of graph networks. We define global and local natural graph networks, the latter of which are as scalable as conventional message passing graph neural networks while being more flexible. We give one practical instantiation of a natural network on graphs which uses an equivariant message network parameterization, yielding good performance on several benchmarks.

Artificial intelligence (AI) has undergone a renaissance recently, making major progress in key domains such as vision, language, control, and decision-making. This has been due, in part, to cheap data and cheap compute resources, which have fit the natural strengths of deep learning. However, many defining characteristics of human intelligence, which developed under much different pressures, remain out of reach for current approaches. In particular, generalizing beyond one's experiences--a hallmark of human intelligence from infancy--remains a formidable challenge for modern AI. The following is part position paper, part review, and part unification. We argue that combinatorial generalization must be a top priority for AI to achieve human-like abilities, and that structured representations and computations are key to realizing this objective. Just as biology uses nature and nurture cooperatively, we reject the false choice between "hand-engineering" and "end-to-end" learning, and instead advocate for an approach which benefits from their complementary strengths. We explore how using relational inductive biases within deep learning architectures can facilitate learning about entities, relations, and rules for composing them. We present a new building block for the AI toolkit with a strong relational inductive bias--the graph network--which generalizes and extends various approaches for neural networks that operate on graphs, and provides a straightforward interface for manipulating structured knowledge and producing structured behaviors. We discuss how graph networks can support relational reasoning and combinatorial generalization, laying the foundation for more sophisticated, interpretable, and flexible patterns of reasoning. As a companion to this paper, we have released an open-source software library for building graph networks, with demonstrations of how to use them in practice.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

Knowledge Graphs (KG) provide us with a structured, flexible, transparent, cross-system, and collaborative way of organizing our knowledge and data across various domains in society and industrial as well as scientific disciplines. KGs surpass any other form of representation in terms of effectiveness. However, Knowledge Graph Engineering (KGE) requires in-depth experiences of graph structures, web technologies, existing models and vocabularies, rule sets, logic, as well as best practices. It also demands a significant amount of work. Considering the advancements in large language models (LLMs) and their interfaces and applications in recent years, we have conducted comprehensive experiments with ChatGPT to explore its potential in supporting KGE. In this paper, we present a selection of these experiments and their results to demonstrate how ChatGPT can assist us in the development and management of KGs.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

Recent advances in question answering have led to substantial progress in tasks such as multi-hop reasoning. However, global sensemaking-answering questions by synthesizing information from an entire corpus remains a significant challenge. A prior graph-based approach to global sensemaking lacks retrieval mechanisms, topic specificity, and incurs high inference costs. To address these limitations, we propose ReTAG, a Retrieval-Enhanced, Topic-Augmented Graph framework that constructs topic-specific subgraphs and retrieves the relevant summaries for response generation. Experiments show that ReTAG improves response quality while significantly reducing inference time compared to the baseline. Our code is available at https://github.com/bykimby/retag.

User profiling has long been an important problem that investigates user interests in many real applications. Some recent works regard users and their interacted objects as entities of a graph and turn the problem into a node classification task. However, they neglect the difference of distinct interaction types, e.g. user clicks an item v.s.user purchases an item, and thus cannot incorporate such information well. To solve these issues, we propose to leverage the relation-aware heterogeneous graph method for user profiling, which also allows capturing significant meta relations. We adopt the query, key, and value mechanism in a transformer fashion for heterogeneous message passing so that entities can effectively interact with each other. Via such interactions on different relation types, our model can generate representations with rich information for the user profile prediction. We conduct experiments on two real-world e-commerce datasets and observe a significant performance boost of our approach.

Multimodal recommender systems utilizing multimodal features (e.g., images and textual descriptions) typically show better recommendation accuracy than general recommendation models based solely on user-item interactions. Generally, prior work fuses multimodal features into item ID embeddings to enrich item representations, thus failing to capture the latent semantic item-item structures. In this context, LATTICE proposes to learn the latent structure between items explicitly and achieves state-of-the-art performance for multimodal recommendations. However, we argue the latent graph structure learning of LATTICE is both inefficient and unnecessary. Experimentally, we demonstrate that freezing its item-item structure before training can also achieve competitive performance. Based on this finding, we propose a simple yet effective model, dubbed as FREEDOM, that FREEzes the item-item graph and DenOises the user-item interaction graph simultaneously for Multimodal recommendation. Theoretically, we examine the design of FREEDOM through a graph spectral perspective and demonstrate that it possesses a tighter upper bound on the graph spectrum. In denoising the user-item interaction graph, we devise a degree-sensitive edge pruning method, which rejects possibly noisy edges with a high probability when sampling the graph. We evaluate the proposed model on three real-world datasets and show that FREEDOM can significantly outperform current strongest baselines. Compared with LATTICE, FREEDOM achieves an average improvement of 19.07% in recommendation accuracy while reducing its memory cost up to 6times on large graphs. The source code is available at: https://github.com/enoche/FREEDOM.

Group Activity Recognition aims to understand collective activities from videos. Existing solutions primarily rely on the RGB modality, which encounters challenges such as background variations, occlusions, motion blurs, and significant computational overhead. Meanwhile, current keypoint-based methods offer a lightweight and informative representation of human motions but necessitate accurate individual annotations and specialized interaction reasoning modules. To address these limitations, we design a panoramic graph that incorporates multi-person skeletons and objects to encapsulate group activity, offering an effective alternative to RGB video. This panoramic graph enables Graph Convolutional Network (GCN) to unify intra-person, inter-person, and person-object interactive modeling through spatial-temporal graph convolutions. In practice, we develop a novel pipeline that extracts skeleton coordinates using pose estimation and tracking algorithms and employ Multi-person Panoramic GCN (MP-GCN) to predict group activities. Extensive experiments on Volleyball and NBA datasets demonstrate that the MP-GCN achieves state-of-the-art performance in both accuracy and efficiency. Notably, our method outperforms RGB-based approaches by using only estimated 2D keypoints as input. Code is available at https://github.com/mgiant/MP-GCN

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Graph Neural Networks (GNNs), especially message-passing neural networks (MPNNs), have emerged as powerful architectures for learning on graphs in diverse applications. However, MPNNs face challenges when modeling non-local interactions in graphs such as large conjugated molecules, and social networks due to oversmoothing and oversquashing. Although Spectral GNNs and traditional neural networks such as recurrent neural networks and transformers mitigate these challenges, they often lack generalizability, or fail to capture detailed structural relationships or symmetries in the data. To address these concerns, we introduce Matrix Function Neural Networks (MFNs), a novel architecture that parameterizes non-local interactions through analytic matrix equivariant functions. Employing resolvent expansions offers a straightforward implementation and the potential for linear scaling with system size. The MFN architecture achieves stateof-the-art performance in standard graph benchmarks, such as the ZINC and TU datasets, and is able to capture intricate non-local interactions in quantum systems, paving the way to new state-of-the-art force fields.

Systems of interacting objects often evolve under the influence of field effects that govern their dynamics, yet previous works have abstracted away from such effects, and assume that systems evolve in a vacuum. In this work, we focus on discovering these fields, and infer them from the observed dynamics alone, without directly observing them. We theorize the presence of latent force fields, and propose neural fields to learn them. Since the observed dynamics constitute the net effect of local object interactions and global field effects, recently popularized equivariant networks are inapplicable, as they fail to capture global information. To address this, we propose to disentangle local object interactions -- which are SE(n) equivariant and depend on relative states -- from external global field effects -- which depend on absolute states. We model interactions with equivariant graph networks, and combine them with neural fields in a novel graph network that integrates field forces. Our experiments show that we can accurately discover the underlying fields in charged particles settings, traffic scenes, and gravitational n-body problems, and effectively use them to learn the system and forecast future trajectories.

Real-world tasks consist of multiple inter-dependent subtasks (e.g., a dirty pan needs to be washed before it can be used for cooking). In this work, we aim to model the causal dependencies between such subtasks from instructional videos describing the task. This is a challenging problem since complete information about the world is often inaccessible from videos, which demands robust learning mechanisms to understand the causal structure of events. We present Multimodal Subtask Graph Generation (MSG2), an approach that constructs a Subtask Graph defining the dependency between a task's subtasks relevant to a task from noisy web videos. Graphs generated by our multimodal approach are closer to human-annotated graphs compared to prior approaches. MSG2 further performs the downstream task of next subtask prediction 85% and 30% more accurately than recent video transformer models in the ProceL and CrossTask datasets, respectively.

Multi-agent systems powered by Large Language Models excel at complex tasks through coordinated collaboration, yet they face high failure rates in multi-turn deep search scenarios. Existing temporal attribution methods struggle to accurately diagnose root causes, particularly when errors propagate across multiple agents. Attempts to automate failure attribution by analyzing action sequences remain ineffective due to their inability to account for information dependencies that span agents. This paper identifies two core challenges: (i) distinguishing symptoms from root causes in multi-agent error propagation, and (ii) tracing information dependencies beyond temporal order. To address these issues, we introduce GraphTracer, a framework that redefines failure attribution through information flow analysis. GraphTracer constructs Information Dependency Graphs (IDGs) to explicitly capture how agents reference and build on prior outputs. It localizes root causes by tracing through these dependency structures instead of relying on temporal sequences. GraphTracer also uses graph-aware synthetic data generation to target critical nodes, creating realistic failure scenarios. Evaluations on the Who\&When benchmark and integration into production systems demonstrate that GraphTracer-8B achieves up to 18.18\% higher attribution accuracy compared to state-of-the-art models and enables 4.8\% to 14.2\% performance improvements in deployed multi-agent frameworks, establishing a robust solution for multi-agent system debugging.

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Higher-order interactions (HOIs) are ubiquitous in real-world complex systems and applications. Investigation of deep learning for HOIs, thus, has become a valuable agenda for the data mining and machine learning communities. As networks of HOIs are expressed mathematically as hypergraphs, hypergraph neural networks (HNNs) have emerged as a powerful tool for representation learning on hypergraphs. Given the emerging trend, we present the first survey dedicated to HNNs, with an in-depth and step-by-step guide. Broadly, the present survey overviews HNN architectures, training strategies, and applications. First, we break existing HNNs down into four design components: (i) input features, (ii) input structures, (iii) message-passing schemes, and (iv) training strategies. Second, we examine how HNNs address and learn HOIs with each of their components. Third, we overview the recent applications of HNNs in recommendation, bioinformatics and medical science, time series analysis, and computer vision. Lastly, we conclude with a discussion on limitations and future directions.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

Volatility forecasting is essential for risk management and decision-making in financial markets. Traditional models like Generalized Autoregressive Conditional Heteroskedasticity (GARCH) effectively capture volatility clustering but often fail to model complex, non-linear interdependencies between multiple indices. This paper proposes a novel approach using Graph Neural Networks (GNNs) to represent global financial markets as dynamic graphs. The Temporal Graph Attention Network (Temporal GAT) combines Graph Convolutional Networks (GCNs) and Graph Attention Networks (GATs) to capture the temporal and structural dynamics of volatility spillovers. By utilizing correlation-based and volatility spillover indices, the Temporal GAT constructs directed graphs that enhance the accuracy of volatility predictions. Empirical results from a 15-year study of eight major global indices show that the Temporal GAT outperforms traditional GARCH models and other machine learning methods, particularly in short- to mid-term forecasts. The sensitivity and scenario-based analysis over a range of parameters and hyperparameters further demonstrate the significance of the proposed technique. Hence, this work highlights the potential of GNNs in modeling complex market behaviors, providing valuable insights for financial analysts and investors.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks(GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily rely on a large amount of task-specific supervision. To reduce labeling requirement, the "pre-train, fine-tune" and "pre-train, prompt" paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-train model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

For a broad range of research, governmental and commercial applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As social media data sets are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present a single-machine real-time system for large-scale graph processing that allows analysts to interactively explore graph structures. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time. We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e. communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetise their data, helping them to continue to provide free services that are valued by billions of people globally.

Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their expansive application in sensitive domains requires a comprehensive understanding of their decision-making processes -- necessitating a framework for GNN explainability. An explanation function for GNNs takes a pre-trained GNN along with a graph as input, to produce a `sufficient statistic' subgraph with respect to the graph label. A main challenge in studying GNN explainability is to provide fidelity measures that evaluate the performance of these explanation functions. This paper studies this foundational challenge, spotlighting the inherent limitations of prevailing fidelity metrics, including Fid_+, Fid_-, and Fid_Delta. Specifically, a formal, information-theoretic definition of explainability is introduced and it is shown that existing metrics often fail to align with this definition across various statistical scenarios. The reason is due to potential distribution shifts when subgraphs are removed in computing these fidelity measures. Subsequently, a robust class of fidelity measures are introduced, and it is shown analytically that they are resilient to distribution shift issues and are applicable in a wide range of scenarios. Extensive empirical analysis on both synthetic and real datasets are provided to illustrate that the proposed metrics are more coherent with gold standard metrics. The source code is available at https://trustai4s-lab.github.io/fidelity.

Large language models (LLMs) are increasingly adopted for a variety of tasks with implicit graphical structures, such as planning in robotics, multi-hop question answering or knowledge probing, structured commonsense reasoning, and more. While LLMs have advanced the state-of-the-art on these tasks with structure implications, whether LLMs could explicitly process textual descriptions of graphs and structures, map them to grounded conceptual spaces, and perform structured operations remains underexplored. To this end, we propose NLGraph (Natural Language Graph), a comprehensive benchmark of graph-based problem solving designed in natural language. NLGraph contains 29,370 problems, covering eight graph reasoning tasks with varying complexity from simple tasks such as connectivity and shortest path up to complex problems such as maximum flow and simulating graph neural networks. We evaluate LLMs (GPT-3/4) with various prompting approaches on the NLGraph benchmark and find that 1) language models do demonstrate preliminary graph reasoning abilities, 2) the benefit of advanced prompting and in-context learning diminishes on more complex graph problems, while 3) LLMs are also (un)surprisingly brittle in the face of spurious correlations in graph and problem settings. We then propose Build-a-Graph Prompting and Algorithmic Prompting, two instruction-based approaches to enhance LLMs in solving natural language graph problems. Build-a-Graph and Algorithmic prompting improve the performance of LLMs on NLGraph by 3.07% to 16.85% across multiple tasks and settings, while how to solve the most complicated graph reasoning tasks in our setup with language models remains an open research question. The NLGraph benchmark and evaluation code are available at https://github.com/Arthur-Heng/NLGraph.

Multitask Gaussian process (MTGP) is powerful for joint learning of multiple tasks with complicated correlation patterns. However, due to the assembling of additive independent latent functions, all current MTGPs including the salient linear model of coregionalization (LMC) and convolution frameworks cannot effectively represent and learn the hierarchical latent interactions between its latent functions. In this paper, we further investigate the interactions in LMC of MTGP and then propose a novel kernel representation of the hierarchical interactions, which ameliorates both the expressiveness and the interpretability of MTGP. Specifically, we express the interaction as a product of function interaction and coefficient interaction. The function interaction is modeled by using cross convolution of latent functions. The coefficient interaction between the LMCs is described as a cross coregionalization term. We validate that considering the interactions can promote knowledge transferring in MTGP and compare our approach with some state-of-the-art MTGPs on both synthetic- and real-world datasets.

Explainable recommendation has demonstrated significant advantages in informing users about the logic behind recommendations, thereby increasing system transparency, effectiveness, and trustworthiness. To provide personalized and interpretable explanations, existing works often combine the generation capabilities of large language models (LLMs) with collaborative filtering (CF) information. CF information extracted from the user-item interaction graph captures the user behaviors and preferences, which is crucial for providing informative explanations. However, due to the complexity of graph structure, effectively extracting the CF information from graphs still remains a challenge. Moreover, existing methods often struggle with the integration of extracted CF information with LLMs due to its implicit representation and the modality gap between graph structures and natural language explanations. To address these challenges, we propose G-Refer, a framework using graph retrieval-augmented large language models (LLMs) for explainable recommendation. Specifically, we first employ a hybrid graph retrieval mechanism to retrieve explicit CF signals from both structural and semantic perspectives. The retrieved CF information is explicitly formulated as human-understandable text by the proposed graph translation and accounts for the explanations generated by LLMs. To bridge the modality gap, we introduce knowledge pruning and retrieval-augmented fine-tuning to enhance the ability of LLMs to process and utilize the retrieved CF information to generate explanations. Extensive experiments show that G-Refer achieves superior performance compared with existing methods in both explainability and stability. Codes and data are available at https://github.com/Yuhan1i/G-Refer.

We address the problem of detecting human-object interactions in images using graphical neural networks. Unlike conventional methods, where nodes send scaled but otherwise identical messages to each of their neighbours, we propose to condition messages between pairs of nodes on their spatial relationships, resulting in different messages going to neighbours of the same node. To this end, we explore various ways of applying spatial conditioning under a multi-branch structure. Through extensive experimentation we demonstrate the advantages of spatial conditioning for the computation of the adjacency structure, messages and the refined graph features. In particular, we empirically show that as the quality of the bounding boxes increases, their coarse appearance features contribute relatively less to the disambiguation of interactions compared to the spatial information. Our method achieves an mAP of 31.33% on HICO-DET and 54.2% on V-COCO, significantly outperforming state-of-the-art on fine-tuned detections.

Generative Agent-Based Modeling (GABM) is an emerging simulation paradigm that combines the reasoning abilities of Large Language Models with traditional Agent-Based Modeling to replicate complex social behaviors, including interactions on social media. While prior work has focused on localized phenomena such as opinion formation and information spread, its potential to capture global network dynamics remains underexplored. This paper addresses this gap by analyzing GABM-based social media simulations through the lens of the Friendship Paradox (FP), a counterintuitive phenomenon where individuals, on average, have fewer friends than their friends. We propose a GABM framework for social media simulations, featuring generative agents that emulate real users with distinct personalities and interests. Using Twitter datasets on the US 2020 Election and the QAnon conspiracy, we show that the FP emerges naturally in GABM simulations. Consistent with real-world observations, the simulations unveil a hierarchical structure, where agents preferentially connect with others displaying higher activity or influence. Additionally, we find that infrequent connections primarily drive the FP, reflecting patterns in real networks. These findings validate GABM as a robust tool for modeling global social media phenomena and highlight its potential for advancing social science by enabling nuanced analysis of user behavior.

Graph Structure Learning (GSL) has recently garnered considerable attention due to its ability to optimize both the parameters of Graph Neural Networks (GNNs) and the computation graph structure simultaneously. Despite the proliferation of GSL methods developed in recent years, there is no standard experimental setting or fair comparison for performance evaluation, which creates a great obstacle to understanding the progress in this field. To fill this gap, we systematically analyze the performance of GSL in different scenarios and develop a comprehensive Graph Structure Learning Benchmark (GSLB) curated from 20 diverse graph datasets and 16 distinct GSL algorithms. Specifically, GSLB systematically investigates the characteristics of GSL in terms of three dimensions: effectiveness, robustness, and complexity. We comprehensively evaluate state-of-the-art GSL algorithms in node- and graph-level tasks, and analyze their performance in robust learning and model complexity. Further, to facilitate reproducible research, we have developed an easy-to-use library for training, evaluating, and visualizing different GSL methods. Empirical results of our extensive experiments demonstrate the ability of GSL and reveal its potential benefits on various downstream tasks, offering insights and opportunities for future research. The code of GSLB is available at: https://github.com/GSL-Benchmark/GSLB.

To provide more accurate, diverse, and explainable recommendation, it is compulsory to go beyond modeling user-item interactions and take side information into account. Traditional methods like factorization machine (FM) cast it as a supervised learning problem, which assumes each interaction as an independent instance with side information encoded. Due to the overlook of the relations among instances or items (e.g., the director of a movie is also an actor of another movie), these methods are insufficient to distill the collaborative signal from the collective behaviors of users. In this work, we investigate the utility of knowledge graph (KG), which breaks down the independent interaction assumption by linking items with their attributes. We argue that in such a hybrid structure of KG and user-item graph, high-order relations --- which connect two items with one or multiple linked attributes --- are an essential factor for successful recommendation. We propose a new method named Knowledge Graph Attention Network (KGAT) which explicitly models the high-order connectivities in KG in an end-to-end fashion. It recursively propagates the embeddings from a node's neighbors (which can be users, items, or attributes) to refine the node's embedding, and employs an attention mechanism to discriminate the importance of the neighbors. Our KGAT is conceptually advantageous to existing KG-based recommendation methods, which either exploit high-order relations by extracting paths or implicitly modeling them with regularization. Empirical results on three public benchmarks show that KGAT significantly outperforms state-of-the-art methods like Neural FM and RippleNet. Further studies verify the efficacy of embedding propagation for high-order relation modeling and the interpretability benefits brought by the attention mechanism.

Understanding the origins of militarized conflict is a complex, yet important undertaking. Existing research seeks to build this understanding by considering bi-lateral relationships between entity pairs (dyadic causes) and multi-lateral relationships among multiple entities (systemic causes). The aim of this work is to compare these two causes in terms of how they correlate with conflict between two entities. We do this by devising a set of textual and graph-based features which represent each of the causes. The features are extracted from Wikipedia and modeled as a large graph. Nodes in this graph represent entities connected by labeled edges representing ally or enemy-relationships. This allows casting the problem as an edge classification task, which we term dyad classification. We propose and evaluate classifiers to determine if a particular pair of entities are allies or enemies. Our results suggest that our systemic features might be slightly better correlates of conflict. Further, we find that Wikipedia articles of allies are semantically more similar than enemies.

This study examines the effects of de-globalization trends on international trade networks and their role in improving forecasts for economic growth. Using section-level trade data from nearly 200 countries from 2010 to 2022, we identify significant shifts in the network topology driven by rising trade policy uncertainty. Our analysis highlights key global players through centrality rankings, with the United States, China, and Germany maintaining consistent dominance. Using a horse race of supervised regressors, we find that network topology descriptors evaluated from section-specific trade networks substantially enhance the quality of a country's GDP growth forecast. We also find that non-linear models, such as Random Forest, XGBoost, and LightGBM, outperform traditional linear models used in the economics literature. Using SHAP values to interpret these non-linear model's predictions, we find that about half of most important features originate from the network descriptors, underscoring their vital role in refining forecasts. Moreover, this study emphasizes the significance of recent economic performance, population growth, and the primary sector's influence in shaping economic growth predictions, offering novel insights into the intricacies of economic growth forecasting.

Multi-modal recommender system focuses on utilizing rich modal information ( i.e., images and textual descriptions) of items to improve recommendation performance. The current methods have achieved remarkable success with the powerful structure modeling capability of graph neural networks. However, these methods are often hindered by sparse data in real-world scenarios. Although contrastive learning and homography ( i.e., homogeneous graphs) are employed to address the data sparsity challenge, existing methods still suffer two main limitations: 1) Simple multi-modal feature contrasts fail to produce effective representations, causing noisy modal-shared features and loss of valuable information in modal-unique features; 2) The lack of exploration of the homograph relations between user interests and item co-occurrence results in incomplete mining of user-item interplay. To address the above limitations, we propose a novel framework for REfining multi-modAl contRastive learning and hoMography relations (REARM). Specifically, we complement multi-modal contrastive learning by employing meta-network and orthogonal constraint strategies, which filter out noise in modal-shared features and retain recommendation-relevant information in modal-unique features. To mine homogeneous relationships effectively, we integrate a newly constructed user interest graph and an item co-occurrence graph with the existing user co-occurrence and item semantic graphs for graph learning. The extensive experiments on three real-world datasets demonstrate the superiority of REARM to various state-of-the-art baselines. Our visualization further shows an improvement made by REARM in distinguishing between modal-shared and modal-unique features. Code is available https://github.com/MrShouxingMa/REARM{here}.

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

Graph convolutional neural networks have recently shown great potential for the task of zero-shot learning. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing generalization to new classes when faced with a lack of data. However, multi-layer architectures, which are required to propagate knowledge to distant nodes in the graph, dilute the knowledge by performing extensive Laplacian smoothing at each layer and thereby consequently decrease performance. In order to still enjoy the benefit brought by the graph structure while preventing dilution of knowledge from distant nodes, we propose a Dense Graph Propagation (DGP) module with carefully designed direct links among distant nodes. DGP allows us to exploit the hierarchical graph structure of the knowledge graph through additional connections. These connections are added based on a node's relationship to its ancestors and descendants. A weighting scheme is further used to weigh their contribution depending on the distance to the node to improve information propagation in the graph. Combined with finetuning of the representations in a two-stage training approach our method outperforms state-of-the-art zero-shot learning approaches.

As multimodal LLM-driven agents continue to advance in autonomy and generalization, evaluation based on static datasets can no longer adequately assess their true capabilities in dynamic environments and diverse tasks. Existing LLM-based synthetic data methods are largely designed for LLM training and evaluation, and thus cannot be directly applied to agent tasks that require tool use and interactive capabilities. While recent studies have explored automatic agent task generation with LLMs, most efforts remain limited to text or image analysis, without systematically modeling multi-step interactions in web environments. To address these challenges, we propose Graph2Eval, a knowledge graph-based framework that automatically generates both multimodal document comprehension tasks and web interaction tasks, enabling comprehensive evaluation of agents' reasoning, collaboration, and interactive capabilities. In our approach, knowledge graphs constructed from multi-source external data serve as the task space, where we translate semantic relations into structured multimodal tasks using subgraph sampling, task templates, and meta-paths. A multi-stage filtering pipeline based on node reachability, LLM scoring, and similarity analysis is applied to guarantee the quality and executability of the generated tasks. Furthermore, Graph2Eval supports end-to-end evaluation of multiple agent types (Single-Agent, Multi-Agent, Web Agent) and measures reasoning, collaboration, and interaction capabilities. We instantiate the framework with Graph2Eval-Bench, a curated dataset of 1,319 tasks spanning document comprehension and web interaction scenarios. Experiments show that Graph2Eval efficiently generates tasks that differentiate agent and model performance, revealing gaps in reasoning, collaboration, and web interaction across different settings and offering a new perspective for agent evaluation.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

The era of foundation models has revolutionized AI research, yet Graph Foundation Models (GFMs) remain constrained by the scarcity of large-scale graph corpora. Traditional graph data synthesis techniques primarily focus on simplistic structural operations, lacking the capacity to generate semantically rich nodes with meaningful textual attributes: a critical limitation for real-world applications. While large language models (LLMs) demonstrate exceptional text generation capabilities, their direct application to graph synthesis is impeded by context window limitations, hallucination phenomena, and structural consistency challenges. To address these issues, we introduce GraphMaster, the first multi-agent framework specifically designed for graph data synthesis in data-limited environments. GraphMaster orchestrates four specialized LLM agents (Manager, Perception, Enhancement, and Evaluation) that collaboratively optimize the synthesis process through iterative refinement, ensuring both semantic coherence and structural integrity. To rigorously evaluate our approach, we create new data-limited "Sub" variants of six standard graph benchmarks, specifically designed to test synthesis capabilities under realistic constraints. Additionally, we develop a novel interpretability assessment framework that combines human evaluation with a principled Grassmannian manifold-based analysis, providing both qualitative and quantitative measures of semantic coherence. Experimental results demonstrate that GraphMaster significantly outperforms traditional synthesis methods across multiple datasets, establishing a strong foundation for advancing GFMs in data-scarce environments.

We study a new connection between a technical measure called mu-conductance that arises in the study of Markov chains for sampling convex bodies and the network community profile that characterizes size-resolved properties of clusters and communities in social and information networks. The idea of mu-conductance is similar to the traditional graph conductance, but disregards sets with small volume. We derive a sequence of optimization problems including a low-rank semi-definite program from which we can derive a lower bound on the optimal mu-conductance value. These ideas give the first theoretically sound bound on the behavior of the network community profile for a wide range of cluster sizes. The algorithm scales up to graphs with hundreds of thousands of nodes and we demonstrate how our framework validates the predicted structures of real-world graphs.

Multi-agent systems (MAS) based on Large Language Models (LLMs) have the potential to solve tasks that are beyond the reach of any single LLM. However, this potential can only be realized when the collaboration mechanism between agents is optimized. Specifically, optimizing the communication structure between agents is critical for fruitful collaboration. Most existing approaches rely on fixed topologies, pretrained graph generators, optimization over edges, or employ external LLM judges, thereby adding to the complexity. In this work, we introduce a response-conditioned framework that adapts communication on-the-fly. Agents independently generate responses to the user query and assess peer contributions using an approximation of the Shapley value. A directed acyclic graph (DAG) is then constructed to regulate the propagation of the responses among agents, which ensures stable and efficient message transmission from high-contributing agents to others. This graph is dynamically updated based on the agent responses from the previous collaboration round. Since the proposed framework enables the self-organization of agents without additional supervision or training, we refer to it as SelfOrg. The SelfOrg framework goes beyond task- and query-level optimization and takes into account the stochastic nature of agent responses. Experiments with both strong and weak LLM backends demonstrate robust performance, with significant gains in the weak regime where prior methods collapse. We also theoretically show that multiple agents increase the chance of correctness and that the correct responses naturally dominate the information flow.

Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data are associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data are paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graph scenarios (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-rich graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we mention the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

Existing foundation models, such as CLIP, aim to learn a unified embedding space for multimodal data, enabling a wide range of downstream web-based applications like search, recommendation, and content classification. However, these models often overlook the inherent graph structures in multimodal datasets, where entities and their relationships are crucial. Multimodal graphs (MMGs) represent such graphs where each node is associated with features from different modalities, while the edges capture the relationships between these entities. On the other hand, existing graph foundation models primarily focus on text-attributed graphs (TAGs) and are not designed to handle the complexities of MMGs. To address these limitations, we propose UniGraph2, a novel cross-domain graph foundation model that enables general representation learning on MMGs, providing a unified embedding space. UniGraph2 employs modality-specific encoders alongside a graph neural network (GNN) to learn a unified low-dimensional embedding space that captures both the multimodal information and the underlying graph structure. We propose a new cross-domain multi-graph pre-training algorithm at scale to ensure effective transfer learning across diverse graph domains and modalities. Additionally, we adopt a Mixture of Experts (MoE) component to align features from different domains and modalities, ensuring coherent and robust embeddings that unify the information across modalities. Extensive experiments on a variety of multimodal graph tasks demonstrate that UniGraph2 significantly outperforms state-of-the-art models in tasks such as representation learning, transfer learning, and multimodal generative tasks, offering a scalable and flexible solution for learning on MMGs.

Knowledge graph is generally incorporated into recommender systems to improve overall performance. Due to the generalization and scale of the knowledge graph, most knowledge relationships are not helpful for a target user-item prediction. To exploit the knowledge graph to capture target-specific knowledge relationships in recommender systems, we need to distill the knowledge graph to reserve the useful information and refine the knowledge to capture the users' preferences. To address the issues, we propose Knowledge-aware Conditional Attention Networks (KCAN), which is an end-to-end model to incorporate knowledge graph into a recommender system. Specifically, we use a knowledge-aware attention propagation manner to obtain the node representation first, which captures the global semantic similarity on the user-item network and the knowledge graph. Then given a target, i.e., a user-item pair, we automatically distill the knowledge graph into the target-specific subgraph based on the knowledge-aware attention. Afterward, by applying a conditional attention aggregation on the subgraph, we refine the knowledge graph to obtain target-specific node representations. Therefore, we can gain both representability and personalization to achieve overall performance. Experimental results on real-world datasets demonstrate the effectiveness of our framework over the state-of-the-art algorithms.

Large language models (LLMs), while exhibiting exceptional performance, suffer from hallucinations, especially on knowledge-intensive tasks. Existing works propose to augment LLMs with individual text units retrieved from external knowledge corpora to alleviate the issue. However, in many domains, texts are interconnected (e.g., academic papers in a bibliographic graph are linked by citations and co-authorships) which form a (text-attributed) graph. The knowledge in such graphs is encoded not only in single texts/nodes but also in their associated connections. To facilitate the research of augmenting LLMs with graphs, we manually construct a Graph Reasoning Benchmark dataset called GRBench, containing 1,740 questions that can be answered with the knowledge from 10 domain graphs. Then, we propose a simple and effective framework called Graph Chain-of-thought (Graph-CoT) to augment LLMs with graphs by encouraging LLMs to reason on the graph iteratively. Each Graph-CoT iteration consists of three sub-steps: LLM reasoning, LLM-graph interaction, and graph execution. We conduct systematic experiments with three LLM backbones on GRBench, where Graph-CoT outperforms the baselines consistently. The code is available at https://github.com/PeterGriffinJin/Graph-CoT.

Multi-view graph clustering (MGC) methods are increasingly being studied due to the explosion of multi-view data with graph structural information. The critical point of MGC is to better utilize view-specific and view-common information in features and graphs of multiple views. However, existing works have an inherent limitation that they are unable to concurrently utilize the consensus graph information across multiple graphs and the view-specific feature information. To address this issue, we propose Variational Graph Generator for Multi-View Graph Clustering (VGMGC). Specifically, a novel variational graph generator is proposed to extract common information among multiple graphs. This generator infers a reliable variational consensus graph based on a priori assumption over multiple graphs. Then a simple yet effective graph encoder in conjunction with the multi-view clustering objective is presented to learn the desired graph embeddings for clustering, which embeds the inferred view-common graph and view-specific graphs together with features. Finally, theoretical results illustrate the rationality of the VGMGC by analyzing the uncertainty of the inferred consensus graph with the information bottleneck principle.Extensive experiments demonstrate the superior performance of our VGMGC over SOTAs. The source code is publicly available at https://github.com/cjpcool/VGMGC.

We introduce Bayesian Poisson Tucker decomposition (BPTD) for modeling country--country interaction event data. These data consist of interaction events of the form "country i took action a toward country j at time t." BPTD discovers overlapping country--community memberships, including the number of latent communities. In addition, it discovers directed community--community interaction networks that are specific to "topics" of action types and temporal "regimes." We show that BPTD yields an efficient MCMC inference algorithm and achieves better predictive performance than related models. We also demonstrate that it discovers interpretable latent structure that agrees with our knowledge of international relations.