Daily Papers

Large Language Models (LLMs) increasingly rely on agentic capabilities-iterative retrieval, tool use, and decision-making-to overcome the limits of static, parametric knowledge. Yet existing agentic frameworks treat external information as unstructured text and fail to leverage the topological dependencies inherent in real-world data. To bridge this gap, we introduce Agentic Graph Learning (AGL), a paradigm that reframes graph learning as an interleaved process of topology-aware navigation and LLM-based inference. Specifically, we propose AgentGL, the first reinforcement learning (RL)-driven framework for AGL. AgentGL equips an LLM agent with graph-native tools for multi-scale exploration, regulates tool usage via search-constrained thinking to balance accuracy and efficiency, and employs a graph-conditioned curriculum RL strategy to stabilize long-horizon policy learning without step-wise supervision. Across diverse Text-Attributed Graph (TAG) benchmarks and multiple LLM backbones, AgentGL substantially outperforms strong GraphLLMs and GraphRAG baselines, achieving absolute improvements of up to 17.5% in node classification and 28.4% in link prediction. These results demonstrate that AGL is a promising frontier for enabling LLMs to autonomously navigate and reason over complex relational environments. The code is publicly available at https://github.com/sunyuanfu/AgentGL.

Recent developments in retrieval-augmented generation (RAG) for selecting relevant tools from a tool knowledge base enable LLM agents to scale their complex tool calling capabilities to hundreds or thousands of external tools, APIs, or agents-as-tools. However, traditional RAG-based tool retrieval fails to capture structured dependencies between tools, limiting the retrieval accuracy of a retrieved tool's dependencies. For example, among a vector database of tools, a "get stock price" API requires a "stock ticker" parameter from a "get stock ticker" API, and both depend on OS-level internet connectivity tools. In this paper, we address this limitation by introducing Graph RAG-Tool Fusion, a novel plug-and-play approach that combines the strengths of vector-based retrieval with efficient graph traversal to capture all relevant tools (nodes) along with any nested dependencies (edges) within the predefined tool knowledge graph. We also present ToolLinkOS, a new tool selection benchmark of 573 fictional tools, spanning over 15 industries, each with an average of 6.3 tool dependencies. We demonstrate that Graph RAG-Tool Fusion achieves absolute improvements of 71.7% and 22.1% over na\"ive RAG on ToolLinkOS and ToolSandbox benchmarks, respectively (mAP@10). ToolLinkOS dataset is available at https://github.com/EliasLumer/Graph-RAG-Tool-Fusion-ToolLinkOS

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

Knowledge graphs have been proven extremely useful in powering diverse applications in semantic search and natural language understanding. In this paper, we present GraphGen4Code, a toolkit to build code knowledge graphs that can similarly power various applications such as program search, code understanding, bug detection, and code automation. GraphGen4Code uses generic techniques to capture code semantics with the key nodes in the graph representing classes, functions, and methods. Edges indicate function usage (e.g., how data flows through function calls, as derived from program analysis of real code), and documentation about functions (e.g., code documentation, usage documentation, or forum discussions such as StackOverflow). Our toolkit uses named graphs in RDF to model graphs per program, or can output graphs as JSON. We show the scalability of the toolkit by applying it to 1.3 million Python files drawn from GitHub, 2,300 Python modules, and 47 million forum posts. This results in an integrated code graph with over 2 billion triples. We make the toolkit to build such graphs as well as the sample extraction of the 2 billion triples graph publicly available to the community for use.

Large Language Models (LLMs) have shown great promise in tool-making, yet existing frameworks often struggle to efficiently construct reliable toolsets and are limited to single-task settings. To address these challenges, we propose GATE (Graph-based Adaptive Tool Evolution), an adaptive framework that dynamically constructs and evolves a hierarchical graph of reusable tools across multiple scenarios. We evaluate GATE on open-ended tasks (Minecraft), agent-based tasks (TextCraft, DABench), and code generation tasks (MATH, Date, TabMWP). Our results show that GATE achieves up to 4.3x faster milestone completion in Minecraft compared to the previous SOTA, and provides an average improvement of 9.23% over existing tool-making methods in code generation tasks and 10.03% in agent tasks. GATE demonstrates the power of adaptive evolution, balancing tool quantity, complexity, and functionality while maintaining high efficiency. Code and data are available at https://github.com/ayanami2003/GATE.

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.

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.

Information graphics are pivotal in effective information dissemination and storytelling. However, creating such graphics is extremely challenging for non-professionals, since the design process requires multifaceted skills and comprehensive knowledge. Thus, despite the many available authoring tools, a significant gap remains in enabling non-experts to produce compelling information graphics seamlessly, especially from scratch. Recent breakthroughs show that Large Language Models (LLMs), especially when tool-augmented, can autonomously engage with external tools, making them promising candidates for enabling innovative graphic design applications. In this work, we propose a LLM-centric interface with the agent GraphiMind for automatic generation, recommendation, and composition of information graphics design resources, based on user intent expressed through natural language. Our GraphiMind integrates a Textual Conversational Interface, powered by tool-augmented LLM, with a traditional Graphical Manipulation Interface, streamlining the entire design process from raw resource curation to composition and refinement. Extensive evaluations highlight our tool's proficiency in simplifying the design process, opening avenues for its use by non-professional users. Moreover, we spotlight the potential of LLMs in reshaping the domain of information graphics design, offering a blend of automation, versatility, and user-centric interactivity.

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.

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.

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.

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.

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.

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.

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.

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

Language models have been effective in a wide range of applications, yet the most sophisticated models are often proprietary. For example, GPT-4 by OpenAI and various models by Anthropic are expensive and consume substantial energy. In contrast, the open-source community has produced competitive models, like Llama3. Furthermore, niche-specific smaller language models, such as those tailored for legal, medical or financial tasks, have outperformed their proprietary counterparts. This paper introduces a novel approach that employs functional tokens to integrate multiple open-source models, each optimized for particular tasks. Our newly developed Octopus v4 model leverages functional tokens to intelligently direct user queries to the most appropriate vertical model and reformat the query to achieve the best performance. Octopus v4, an evolution of the Octopus v1, v2, and v3 models, excels in selection and parameter understanding and reformatting. Additionally, we explore the use of graph as a versatile data structure that effectively coordinates multiple open-source models by harnessing the capabilities of the Octopus model and functional tokens. Use our open-sourced GitHub (https://www.nexa4ai.com/) to try Octopus v4 models (https://huggingface.co/NexaAIDev/Octopus-v4), and contrite to a larger graph of language models. By activating models less than 10B parameters, we achieved SOTA MMLU score of 74.8 among the same level models.

This paper presents a novel framework for automated code generation and debugging, designed to improve accuracy, efficiency, and scalability in software development. The proposed system integrates three core components LangGraph, GLM4 Flash, and ChromaDB within a four step iterative workflow to deliver robust performance and seamless functionality. LangGraph serves as a graph-based library for orchestrating tasks, providing precise control and execution while maintaining a unified state object for dynamic updates and consistency. It supports multi-agent, hierarchical, and sequential processes, making it highly adaptable to complex software engineering workflows. GLM4 Flash, a large language model, leverages its advanced capabilities in natural language understanding, contextual reasoning, and multilingual support to generate accurate code snippets based on user prompts. ChromaDB acts as a vector database for semantic search and contextual memory storage, enabling the identification of patterns and the generation of context-aware bug fixes based on historical data. The system operates through a structured four-step process: (1) Code Generation, which translates natural language descriptions into executable code; (2) Code Execution, which validates the code by identifying runtime errors and inconsistencies; (3) Code Repair, which iteratively refines buggy code using ChromaDB's memory capabilities and LangGraph's state tracking; and (4) Code Update, which ensures the code meets functional and performance requirements through iterative modifications.

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.

This work aims to tackle the challenging heterogeneous graph encoding problem in the text-to-SQL task. Previous methods are typically node-centric and merely utilize different weight matrices to parameterize edge types, which 1) ignore the rich semantics embedded in the topological structure of edges, and 2) fail to distinguish local and non-local relations for each node. To this end, we propose a Line Graph Enhanced Text-to-SQL (LGESQL) model to mine the underlying relational features without constructing meta-paths. By virtue of the line graph, messages propagate more efficiently through not only connections between nodes, but also the topology of directed edges. Furthermore, both local and non-local relations are integrated distinctively during the graph iteration. We also design an auxiliary task called graph pruning to improve the discriminative capability of the encoder. Our framework achieves state-of-the-art results (62.8% with Glove, 72.0% with Electra) on the cross-domain text-to-SQL benchmark Spider at the time of writing.

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.

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.

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.

Large language models (LLMs) like ChatGPT, exhibit powerful zero-shot and instruction-following capabilities, have catalyzed a revolutionary transformation across diverse fields, especially for open-ended tasks. While the idea is less explored in the graph domain, despite the availability of numerous powerful graph models (GMs), they are restricted to tasks in a pre-defined form. Although several methods applying LLMs to graphs have been proposed, they fail to simultaneously handle the pre-defined and open-ended tasks, with LLM as a node feature enhancer or as a standalone predictor. To break this dilemma, we propose to bridge the pretrained GM and LLM by a Translator, named GraphTranslator, aiming to leverage GM to handle the pre-defined tasks effectively and utilize the extended interface of LLMs to offer various open-ended tasks for GM. To train such Translator, we propose a Producer capable of constructing the graph-text alignment data along node information, neighbor information and model information. By translating node representation into tokens, GraphTranslator empowers an LLM to make predictions based on language instructions, providing a unified perspective for both pre-defined and open-ended tasks. Extensive results demonstrate the effectiveness of our proposed GraphTranslator on zero-shot node classification. The graph question answering experiments reveal our GraphTranslator potential across a broad spectrum of open-ended tasks through language instructions. Our code is available at: https://github.com/alibaba/GraphTranslator.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

Although there exist several libraries for deep learning on graphs, they are aiming at implementing basic operations for graph deep learning. In the research community, implementing and benchmarking various advanced tasks are still painful and time-consuming with existing libraries. To facilitate graph deep learning research, we introduce DIG: Dive into Graphs, a turnkey library that provides a unified testbed for higher level, research-oriented graph deep learning tasks. Currently, we consider graph generation, self-supervised learning on graphs, explainability of graph neural networks, and deep learning on 3D graphs. For each direction, we provide unified implementations of data interfaces, common algorithms, and evaluation metrics. Altogether, DIG is an extensible, open-source, and turnkey library for researchers to develop new methods and effortlessly compare with common baselines using widely used datasets and evaluation metrics. Source code is available at https://github.com/divelab/DIG.

Human intelligence naturally intertwines omni-modal perception -- spanning vision, audio, and language -- with complex reasoning and tool usage to interact with the world. However, current multi-modal LLMs are primarily confined to bi-modal interactions (e.g., vision-language), lacking the unified cognitive capabilities required for general AI assistants. To bridge this gap, we introduce OmniGAIA, a comprehensive benchmark designed to evaluate omni-modal agents on tasks necessitating deep reasoning and multi-turn tool execution across video, audio, and image modalities. Constructed via a novel omni-modal event graph approach, OmniGAIA synthesizes complex, multi-hop queries derived from real-world data that require cross-modal reasoning and external tool integration. Furthermore, we propose OmniAtlas, a native omni-modal foundation agent under tool-integrated reasoning paradigm with active omni-modal perception. Trained on trajectories synthesized via a hindsight-guided tree exploration strategy and OmniDPO for fine-grained error correction, OmniAtlas effectively enhances the tool-use capabilities of existing open-source models. This work marks a step towards next-generation native omni-modal AI assistants for real-world scenarios.

Deploying dynamic heterogeneous graph embeddings in production faces key challenges of scalability, data freshness, and cold-start. This paper introduces a practical, two-stage solution that balances deep graph representation with low-latency incremental updates. Our framework combines HetSGFormer, a scalable graph transformer for static learning, with Incremental Locally Linear Embedding (ILLE), a lightweight, CPU-based algorithm for real-time updates. HetSGFormer captures global structure with linear scalability, while ILLE provides rapid, targeted updates to incorporate new data, thus avoiding costly full retraining. This dual approach is cold-start resilient, leveraging the graph to create meaningful embeddings from sparse data. On billion-scale graphs, A/B tests show HetSGFormer achieved up to a 6.11% lift in Advertiser Value over previous methods, while the ILLE module added another 3.22% lift and improved embedding refresh timeliness by 83.2%. Our work provides a validated framework for deploying dynamic graph learning in production environments.

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.

Given a node-attributed graph, and a graph task (link prediction or node classification), can we tell if a graph neural network (GNN) will perform well? More specifically, do the graph structure and the node features carry enough usable information for the task? Our goals are (1) to develop a fast tool to measure how much information is in the graph structure and in the node features, and (2) to exploit the information to solve the task, if there is enough. We propose NetInfoF, a framework including NetInfoF_Probe and NetInfoF_Act, for the measurement and the exploitation of network usable information (NUI), respectively. Given a graph data, NetInfoF_Probe measures NUI without any model training, and NetInfoF_Act solves link prediction and node classification, while two modules share the same backbone. In summary, NetInfoF has following notable advantages: (a) General, handling both link prediction and node classification; (b) Principled, with theoretical guarantee and closed-form solution; (c) Effective, thanks to the proposed adjustment to node similarity; (d) Scalable, scaling linearly with the input size. In our carefully designed synthetic datasets, NetInfoF correctly identifies the ground truth of NUI and is the only method being robust to all graph scenarios. Applied on real-world datasets, NetInfoF wins in 11 out of 12 times on link prediction compared to general GNN baselines.

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.

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.

Retrieval-augmented generation (RAG) empowers large language models to access external and private corpus, enabling factually consistent responses in specific domains. By exploiting the inherent structure of the corpus, graph-based RAG methods further enrich this process by building a knowledge graph index and leveraging the structural nature of graphs. However, current graph-based RAG approaches seldom prioritize the design of graph structures. Inadequately designed graph not only impede the seamless integration of diverse graph algorithms but also result in workflow inconsistencies and degraded performance. To further unleash the potential of graph for RAG, we propose NodeRAG, a graph-centric framework introducing heterogeneous graph structures that enable the seamless and holistic integration of graph-based methodologies into the RAG workflow. By aligning closely with the capabilities of LLMs, this framework ensures a fully cohesive and efficient end-to-end process. Through extensive experiments, we demonstrate that NodeRAG exhibits performance advantages over previous methods, including GraphRAG and LightRAG, not only in indexing time, query time, and storage efficiency but also in delivering superior question-answering performance on multi-hop benchmarks and open-ended head-to-head evaluations with minimal retrieval tokens. Our GitHub repository could be seen at https://github.com/Terry-Xu-666/NodeRAG.

Large language models (LLMs) have shown promising capabilities in using external tools to solve complex problems. However, existing approaches either involve fine-tuning on tool demonstrations, which do not generalize to new tools without additional training, or providing tool documentation in context, limiting the number of tools. Both approaches often generate syntactically invalid tool calls. In this paper, we propose ToolDec, a finite-state machine-guided decoding algorithm for tool-augmented LLMs. ToolDec eliminates tool-related errors for any tool-augmented LLMs by ensuring valid tool names and type-conforming arguments. Furthermore, ToolDec enables LLM to effectively select tools using only the information contained in their names, with no need for fine-tuning or in-context documentation. We evaluated multiple prior methods and their ToolDec-enhanced versions on a variety of tasks involving tools like math functions, knowledge graph relations, and complex real-world RESTful APIs. Our experiments show that ToolDec reduces syntactic errors to zero, consequently achieving significantly better performance and as much as a 2x speedup. We also show that ToolDec achieves superior generalization performance on unseen tools, performing up to 8x better than the baselines.

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models, and explaining predictions made by GNNs remains unsolved. Here we propose GNNExplainer, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GNNExplainer identifies a compact subgraph structure and a small subset of node features that have a crucial role in GNN's prediction. Further, GNNExplainer can generate consistent and concise explanations for an entire class of instances. We formulate GNNExplainer as an optimization task that maximizes the mutual information between a GNN's prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms baselines by 17.1% on average. GNNExplainer provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.

Graphs are a fundamental data structure for representing relationships in real-world scenarios. With the success of Large Language Models (LLMs) across various natural language processing (NLP) tasks, there has been growing interest in integrating LLMs for graph learning. However, applying LLMs to graph-related tasks poses significant challenges, as these models are not inherently designed to capture the complex structural information present in graphs. Existing approaches address this challenge through two strategies: the chain of tasks approach, which uses Graph Neural Networks (GNNs) to encode the graph structure so that LLMs are relieved from understanding spatial positions; and Graph-to-Text Conversion, which translates graph structures into semantic text representations that LLMs can process. Despite their progress, these methods often struggle to fully preserve the topological information of graphs or require extensive computational resources, limiting their practical applicability. In this work, we introduce Node Tokenizer for Large Language Models (NT-LLM), a novel framework that efficiently encodes graph structures by selecting key nodes as anchors and representing each node based on its relative distance to these anchors. This position-anchored encoding effectively captures the graph topology, enabling enhanced reasoning capabilities in LLMs over graph data. Additionally, we implement a task-specific tuning procedure to further improve structural understanding within LLMs. Through extensive empirical evaluations, NT-LLM demonstrates significant performance improvements across a variety of graph-related tasks.

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.

The growing demand for automated graph algorithm reasoning has attracted increasing attention in the large language model (LLM) community. Recent LLM-based graph reasoning methods typically decouple task descriptions from graph data, generate executable code augmented by retrieval from technical documentation, and refine the code through debugging. However, we identify two key limitations in existing approaches: (i) they treat technical documentation as flat text collections and ignore its hierarchical structure, leading to noisy retrieval that degrades code generation quality; and (ii) their debugging mechanisms focus primarily on runtime errors, yet ignore more critical logical errors. To address them, we propose {\method}, an agentic hierarchical retrieval-augmented coding framework that exploits the document hierarchy through top-down traversal and early pruning, together with a self-debugging coding agent that iteratively refines code using automatically generated small-scale test cases. To enable comprehensive evaluation of complex graph reasoning, we introduce a new dataset, {\dataset}, covering small-scale, large-scale, and composite graph reasoning tasks. Extensive experiments demonstrate that our method achieves higher task accuracy and lower inference cost compared to baselinesThe code is available at \href{https://github.com/FairyFali/GraphSkill{blue{https://github.com/FairyFali/GraphSkill}}.}.

Large Language Models (LLMs) have demonstrated their potential in hardware design tasks, such as Hardware Description Language (HDL) generation and debugging. Yet, their performance in real-world, repository-level HDL projects with thousands or even tens of thousands of code lines is hindered. To this end, we propose HDLxGraph, a novel framework that integrates Graph Retrieval Augmented Generation (Graph RAG) with LLMs, introducing HDL-specific graph representations by incorporating Abstract Syntax Trees (ASTs) and Data Flow Graphs (DFGs) to capture both code graph view and hardware graph view. HDLxGraph utilizes a dual-retrieval mechanism that not only mitigates the limited recall issues inherent in similarity-based semantic retrieval by incorporating structural information, but also enhances its extensibility to various real-world tasks by a task-specific retrieval finetuning. Additionally, to address the lack of comprehensive HDL search benchmarks, we introduce HDLSearch, a multi-granularity evaluation dataset derived from real-world repository-level projects. Experimental results demonstrate that HDLxGraph significantly improves average search accuracy, debugging efficiency and completion quality by 12.04%, 12.22% and 5.04% compared to similarity-based RAG, respectively. The code of HDLxGraph and collected HDLSearch benchmark are available at https://github.com/Nick-Zheng-Q/HDLxGraph.

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.

Recently, integrating external tools with Large Language Models (LLMs) has gained significant attention as an effective strategy to mitigate the limitations inherent in their pre-training data. However, real-world systems often incorporate a wide array of tools, making it impractical to input all tools into LLMs due to length limitations and latency constraints. Therefore, to fully exploit the potential of tool-augmented LLMs, it is crucial to develop an effective tool retrieval system. Existing tool retrieval methods primarily focus on semantic matching between user queries and tool descriptions, frequently leading to the retrieval of redundant, similar tools. Consequently, these methods fail to provide a complete set of diverse tools necessary for addressing the multifaceted problems encountered by LLMs. In this paper, we propose a novel modelagnostic COllaborative Learning-based Tool Retrieval approach, COLT, which captures not only the semantic similarities between user queries and tool descriptions but also takes into account the collaborative information of tools. Specifically, we first fine-tune the PLM-based retrieval models to capture the semantic relationships between queries and tools in the semantic learning stage. Subsequently, we construct three bipartite graphs among queries, scenes, and tools and introduce a dual-view graph collaborative learning framework to capture the intricate collaborative relationships among tools during the collaborative learning stage. Extensive experiments on both the open benchmark and the newly introduced ToolLens dataset show that COLT achieves superior performance. Notably, the performance of BERT-mini (11M) with our proposed model framework outperforms BERT-large (340M), which has 30 times more parameters. Furthermore, we will release ToolLens publicly to facilitate future research on tool retrieval.

The growing importance of textual and relational systems has driven interest in enhancing large language models (LLMs) for graph-structured data, particularly Text-Attributed Graphs (TAGs), where samples are represented by textual descriptions interconnected by edges. While research has largely focused on developing specialized graph LLMs through task-specific instruction tuning, a comprehensive benchmark for evaluating LLMs solely through prompt design remains surprisingly absent. Without such a carefully crafted evaluation benchmark, most if not all, tailored graph LLMs are compared against general LLMs using simplistic queries (e.g., zero-shot reasoning with LLaMA), which can potentially camouflage many advantages as well as unexpected predicaments of them. To achieve more general evaluations and unveil the true potential of LLMs for graph tasks, we introduce Graph In-context Learning (GraphICL) Benchmark, a comprehensive benchmark comprising novel prompt templates designed to capture graph structure and handle limited label knowledge. Our systematic evaluation shows that general-purpose LLMs equipped with our GraphICL outperform state-of-the-art specialized graph LLMs and graph neural network models in resource-constrained settings and out-of-domain tasks. These findings highlight the significant potential of prompt engineering to enhance LLM performance on graph learning tasks without training and offer a strong baseline for advancing research in graph LLMs.

Large Language Model (LLM) agents have emerged as powerful tools for automating complex tasks by leveraging the reasoning and decision-making abilities of LLMs. However, a major bottleneck in current agent frameworks lies in the high inference cost of tool selection, especially in approaches like ReAct that repeatedly invoke the LLM to determine which tool to use at each step. In this work, we propose AutoTool, a novel graph-based framework that bypasses repeated LLM inference by exploiting a key empirical observation: tool usage inertia - the tendency of tool invocations to follow predictable sequential patterns. AutoTool constructs a directed graph from historical agent trajectories, where nodes represent tools and edges capture transition probabilities, effectively modeling the inertia in tool selection. It further integrates parameter-level information to refine tool input generation. By traversing this structured representation, AutoTool efficiently selects tools and their parameters with minimal reliance on LLM inference. Extensive experiments across diverse agent tasks demonstrate that AutoTool reduces inference costs by up to 30% while maintaining competitive task completion rates, offering a practical and scalable enhancement for inference-heavy frameworks. Our work highlights the promise of integrating statistical structure into LLM agent design for greater efficiency without sacrificing performance.

Evaluating and enhancing the general capabilities of large language models (LLMs) has been an important research topic. Graph is a common data structure in the real world, and understanding graph data is a crucial part for advancing general intelligence. To evaluate and enhance the graph understanding abilities of LLMs, in this paper, we propose a benchmark named GraphInstruct, which comprehensively includes 21 classical graph reasoning tasks, providing diverse graph generation pipelines and detailed reasoning steps. Based on GraphInstruct, we further construct GraphLM through efficient instruction-tuning, which shows prominent graph understanding capability. In order to enhance the LLM with graph reasoning capability as well, we propose a step mask training strategy, and construct a model named GraphLM+. As one of the pioneering efforts to enhance the graph understanding and reasoning abilities of LLMs, extensive experiments have demonstrated the superiority of GraphLM and GraphLM+ over other LLMs. We look forward to more researchers exploring the potential of LLMs in the graph data mining domain through GraphInstruct. Our code for generating GraphInstruct is released publicly at: https://github.com/CGCL-codes/GraphInstruct.

Although Large Language Models (LLMs) have demonstrated potential in processing graphs, they struggle with comprehending graphical structure information through prompts of graph description sequences, especially as the graph size increases. We attribute this challenge to the uneven memory performance of LLMs across different positions in graph description sequences, known as ''positional biases''. To address this, we propose GraphInsight, a novel framework aimed at improving LLMs' comprehension of both macro- and micro-level graphical information. GraphInsight is grounded in two key strategies: 1) placing critical graphical information in positions where LLMs exhibit stronger memory performance, and 2) investigating a lightweight external knowledge base for regions with weaker memory performance, inspired by retrieval-augmented generation (RAG). Moreover, GraphInsight explores integrating these two strategies into LLM agent processes for composite graph tasks that require multi-step reasoning. Extensive empirical studies on benchmarks with a wide range of evaluation tasks show that GraphInsight significantly outperforms all other graph description methods (e.g., prompting techniques and reordering strategies) in understanding graph structures of varying sizes.

Can we model non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The non-Euclidean property have posed a long term challenge in graph modeling. Despite recent GNN and Graphformer efforts encoding graphs as Euclidean vectors, recovering original graph from the vectors remains a challenge. We introduce GraphsGPT, featuring a Graph2Seq encoder that transforms non-Euclidean graphs into learnable graph words in a Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from graph words to ensure information equivalence. We pretrain GraphsGPT on 100M molecules and yield some interesting findings: (1) Pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on 8/9 graph classification and regression tasks. (2) Pretrained GraphGPT serves as a strong graph generator, demonstrated by its ability to perform both unconditional and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known non-Euclidean challenge. (4) Our proposed novel edge-centric GPT pretraining task is effective in graph fields, underscoring its success in both representation and generation.

Heterogeneous graph learning aims to capture complex relationships and diverse relational semantics among entities in a heterogeneous graph to obtain meaningful representations for nodes and edges. Recent advancements in heterogeneous graph neural networks (HGNNs) have achieved state-of-the-art performance by considering relation heterogeneity and using specialized message functions and aggregation rules. However, existing frameworks for heterogeneous graph learning have limitations in generalizing across diverse heterogeneous graph datasets. Most of these frameworks follow the "pre-train" and "fine-tune" paradigm on the same dataset, which restricts their capacity to adapt to new and unseen data. This raises the question: "Can we generalize heterogeneous graph models to be well-adapted to diverse downstream learning tasks with distribution shifts in both node token sets and relation type heterogeneity?'' To tackle those challenges, we propose HiGPT, a general large graph model with Heterogeneous graph instruction-tuning paradigm. Our framework enables learning from arbitrary heterogeneous graphs without the need for any fine-tuning process from downstream datasets. To handle distribution shifts in heterogeneity, we introduce an in-context heterogeneous graph tokenizer that captures semantic relationships in different heterogeneous graphs, facilitating model adaptation. We incorporate a large corpus of heterogeneity-aware graph instructions into our HiGPT, enabling the model to effectively comprehend complex relation heterogeneity and distinguish between various types of graph tokens. Furthermore, we introduce the Mixture-of-Thought (MoT) instruction augmentation paradigm to mitigate data scarcity by generating diverse and informative instructions. Through comprehensive evaluations, our proposed framework demonstrates exceptional performance in terms of generalization performance.

Graphs are ubiquitous structures found in numerous real-world applications, such as drug discovery, recommender systems, and social network analysis. To model graph-structured data, graph neural networks (GNNs) have become a popular tool. However, existing GNN architectures encounter challenges in cross-graph learning where multiple graphs have different feature spaces. To address this, recent approaches introduce text-attributed graphs (TAGs), where each node is associated with a textual description, which can be projected into a unified feature space using textual encoders. While promising, this method relies heavily on the availability of text-attributed graph data, which is difficult to obtain in practice. To bridge this gap, we propose a novel method named Topology-Aware Node description Synthesis (TANS), leveraging large language models (LLMs) to convert existing graphs into text-attributed graphs. The key idea is to integrate topological information into LLMs to explain how graph topology influences node semantics. We evaluate our TANS on text-rich, text-limited, and text-free graphs, demonstrating its applicability. Notably, on text-free graphs, our method significantly outperforms existing approaches that manually design node features, showcasing the potential of LLMs for preprocessing graph-structured data in the absence of textual information. The code and data are available at https://github.com/Zehong-Wang/TANS.

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these structured representations given new sources of information. Although there have been many efforts focusing on improving the performance of the parsers that map text to graphs or parse trees, very few have explored the problem of directly manipulating these representations. In this paper, we explore the novel problem of graph modification, where the systems need to learn how to update an existing scene graph given a new user's command. Our novel models based on graph-based sparse transformer and cross attention information fusion outperform previous systems adapted from the machine translation and graph generation literature. We further contribute our large graph modification datasets to the research community to encourage future research for this new problem.

Program source code contains complex structure information, which can be represented in structured data forms like trees or graphs. To acquire the structural information in source code, most existing researches use abstract syntax trees (AST). A group of works add additional edges to ASTs to convert source code into graphs and use graph neural networks to learn representations for program graphs. Although these works provide additional control or data flow information to ASTs for downstream tasks, they neglect an important aspect of structure information in AST itself: the different types of nodes and edges. In ASTs, different nodes contain different kinds of information like variables or control flow, and the relation between a node and all its children can also be different. To address the information of node and edge types, we bring the idea of heterogeneous graphs to learning on source code and present a new formula of building heterogeneous program graphs from ASTs with additional type information for nodes and edges. We use the ASDL grammar of programming language to define the node and edge types of program graphs. Then we use heterogeneous graph neural networks to learn on these graphs. We evaluate our approach on two tasks: code comment generation and method naming. Both tasks require reasoning on the semantics of complete code snippets. Experiment results show that our approach outperforms baseline models, including homogeneous graph-based models, showing that leveraging the type information of nodes and edges in program graphs can help in learning program semantics.

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.

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.

Tool-using LLM agents face a reliability-cost tradeoff: routing every decision through the LLM improves correctness but incurs high latency and inference cost, while pre-coded workflow graphs reduce cost but become brittle under unanticipated compound tool failures. We present Self-Healing Router, a fault-tolerant orchestration architecture that treats most agent control-flow decisions as routing rather than reasoning. The system combines (i) parallel health monitors that assign priority scores to runtime conditions such as tool outages and risk signals, and (ii) a cost-weighted tool graph where Dijkstra's algorithm performs deterministic shortest-path routing. When a tool fails mid-execution, its edges are reweighted to infinity and the path is recomputed -- yielding automatic recovery without invoking the LLM. The LLM is reserved exclusively for cases where no feasible path exists, enabling goal demotion or escalation. Prior graph-based tool-use systems (ControlLLM, ToolNet, NaviAgent) focus on tool selection and planning; our contribution is runtime fault tolerance with deterministic recovery and binary observability -- every failure is either a logged reroute or an explicit escalation, never a silent skip. Across 19 scenarios spanning three graph topologies (linear pipeline, dependency DAG, parallel fan-out), Self-Healing Router matches ReAct's correctness while reducing control-plane LLM calls by 93% (9 vs 123 aggregate) and eliminating the silent-failure cases observed in a well-engineered static workflow baseline under compound failures.

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field.

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.

Diffusion-based generative graph models have been proven effective in generating high-quality small graphs. However, they need to be more scalable for generating large graphs containing thousands of nodes desiring graph statistics. In this work, we propose EDGE, a new diffusion-based generative graph model that addresses generative tasks with large graphs. To improve computation efficiency, we encourage graph sparsity by using a discrete diffusion process that randomly removes edges at each time step and finally obtains an empty graph. EDGE only focuses on a portion of nodes in the graph at each denoising step. It makes much fewer edge predictions than previous diffusion-based models. Moreover, EDGE admits explicitly modeling the node degrees of the graphs, further improving the model performance. The empirical study shows that EDGE is much more efficient than competing methods and can generate large graphs with thousands of nodes. It also outperforms baseline models in generation quality: graphs generated by our approach have more similar graph statistics to those of the training graphs.

In recent years, large language models (LLMs) have emerged as promising candidates for graph tasks. Many studies leverage natural language to describe graphs and apply LLMs for reasoning, yet most focus narrowly on performance benchmarks without fully comparing LLMs to graph learning models or exploring their broader potential. In this work, we present a comprehensive study of LLMs on graph learning tasks, evaluating both off-the-shelf and instruction-tuned models across a variety of scenarios. Beyond accuracy, we discuss data leakage concerns and computational overhead, and assess their performance under few-shot/zero-shot settings, domain transfer, structural understanding, and robustness. Our findings show that LLMs, particularly those with instruction tuning, greatly outperform traditional graph learning models in few-shot settings, exhibit strong domain transferability, and demonstrate excellent generalization and robustness. Our study highlights the broader capabilities of LLMs in graph learning and provides a foundation for future research.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

Graph Neural Architecture Search (GNAS) facilitates the automatic design of Graph Neural Networks (GNNs) tailored to specific downstream graph learning tasks. However, existing GNAS approaches often require manual adaptation to new graph search spaces, necessitating substantial code optimization and domain-specific knowledge. To address this challenge, we present LLM4GNAS, a toolkit for GNAS that leverages the generative capabilities of Large Language Models (LLMs). LLM4GNAS includes an algorithm library for graph neural architecture search algorithms based on LLMs, enabling the adaptation of GNAS methods to new search spaces through the modification of LLM prompts. This approach reduces the need for manual intervention in algorithm adaptation and code modification. The LLM4GNAS toolkit is extensible and robust, incorporating LLM-enhanced graph feature engineering, LLM-enhanced graph neural architecture search, and LLM-enhanced hyperparameter optimization. Experimental results indicate that LLM4GNAS outperforms existing GNAS methods on tasks involving both homogeneous and heterogeneous graphs.

Acceleration of graph applications on GPUs has found large interest due to the ubiquitous use of graph processing in various domains. The inherent irregularity in graph applications leads to several challenges for parallelization. A key challenge, which we address in this paper, is that of load-imbalance. If the work-assignment to threads uses node-based graph partitioning, it can result in skewed task-distribution, leading to poor load-balance. In contrast, if the work-assignment uses edge-based graph partitioning, the load-balancing is better, but the memory requirement is relatively higher. This makes it unsuitable for large graphs. In this work, we propose three techniques for improved load-balancing of graph applications on GPUs. Each technique brings in unique advantages, and a user may have to employ a specific technique based on the requirement. Using Breadth First Search and Single Source Shortest Paths as our processing kernels, we illustrate the effectiveness of each of the proposed techniques in comparison to the existing node-based and edge-based mechanisms.

Given a massive graph, how can we exploit its hierarchical structure for concisely but exactly summarizing the graph? By exploiting the structure, can we achieve better compression rates than state-of-the-art graph summarization methods? The explosive proliferation of the Web has accelerated the emergence of large graphs, such as online social networks and hyperlink networks. Consequently, graph compression has become increasingly important to process such large graphs without expensive I/O over the network or to disk. Among a number of approaches, graph summarization, which in essence combines similar nodes into a supernode and describe their connectivity concisely, protrudes with several advantages. However, we note that it fails to exploit pervasive hierarchical structures of real-world graphs as its underlying representation model enforces supernodes to be disjoint. In this work, we propose the hierarchical graph summarization model, which is an expressive graph representation model that includes the previous one proposed by Navlakha et al. as a special case. The new model represents an unweighted graph using positive and negative edges between hierarchical supernodes, each of which can contain others. Then, we propose Slugger, a scalable heuristic for concisely and exactly representing a given graph under our new model. Slugger greedily merges nodes into supernodes while maintaining and exploiting their hierarchy, which is later pruned. Slugger significantly accelerates this process by sampling, approximation, and memoization. Our experiments on 16 real-world graphs show that Slugger is (a) Effective: yielding up to 29.6% more concise summary than state-of-the-art lossless summarization methods, (b) Fast: summarizing a graph with 0.8 billion edges in a few hours, and (c) Scalable: scaling linearly with the number of edges in the input graph.

Relational databases (RDBs) are composed of interconnected tables, where relationships between them are defined through foreign keys. Recent research on applying machine learning to RDBs has explored graph-based representations of RDBs, where rows of tables are modeled as nodes, and foreign key relationships are modeled as edges. RDB-to-graph modeling helps capture cross-table dependencies, ultimately leading to enhanced performance across diverse tasks. However, there are numerous ways to model RDBs as graphs, and performance varies significantly depending on the chosen graph model. In our analysis, applying a common heuristic rule for graph modeling leads to up to a 10% drop in performance compared to the best-performing graph model, which remains non-trivial to identify. To foster research on intelligent RDB-to-graph modeling, we introduce RDB2G-Bench, the first benchmark framework for evaluating such methods. We construct extensive datasets covering 5 real-world RDBs and 12 predictive tasks, resulting in around 50k graph-performance pairs for efficient and reproducible evaluations. Thanks to our precomputed datasets, we were able to benchmark 9 automatic RDB-to-graph modeling methods on the 12 tasks over 600x faster than on-the-fly evaluation, which requires repeated model training. Our analysis of the datasets and benchmark results reveals key structural patterns affecting graph model effectiveness, along with practical implications for effective graph modeling.

The automated extraction of complete and precise road network graphs from remote sensing imagery remains a critical challenge in geospatial computer vision. Segmentation-based approaches, while effective in pixel-level recognition, struggle to maintain topology fidelity after vectorization postprocessing. Graph-growing methods build more topologically faithful graphs but suffer from computationally prohibitive iterative ROI cropping. Graph-generating methods first predict global static candidate road network vertices, and then infer possible edges between vertices. They achieve fast topology-aware inference, but limits the dynamic insertion of vertices. To address these challenges, we propose DeH4R, a novel hybrid model that combines graph-generating efficiency and graph-growing dynamics. This is achieved by decoupling the task into candidate vertex detection, adjacent vertex prediction, initial graph contruction, and graph expansion. This architectural innovation enables dynamic vertex (edge) insertions while retaining fast inference speed and enhancing both topology fidelity and spatial consistency. Comprehensive evaluations on CityScale and SpaceNet benchmarks demonstrate state-of-the-art (SOTA) performance. DeH4R outperforms the prior SOTA graph-growing method RNGDet++ by 4.62 APLS and 10.18 IoU on CityScale, while being approximately 10 times faster. The code will be made publicly available at https://github.com/7777777FAN/DeH4R.

With the rapid increase in the amount of public code repositories, developers maintain a great desire to retrieve precise code snippets by using natural language. Despite existing deep learning based approaches(e.g., DeepCS and MMAN) have provided the end-to-end solutions (i.e., accepts natural language as queries and shows related code fragments retrieved directly from code corpus), the accuracy of code search in the large-scale repositories is still limited by the code representation (e.g., AST) and modeling (e.g., directly fusing the features in the attention stage). In this paper, we propose a novel learnable deep Graph for Code Search (calleddeGraphCS), to transfer source code into variable-based flow graphs based on the intermediate representation technique, which can model code semantics more precisely compared to process the code as text directly or use the syntactic tree representation. Furthermore, we propose a well-designed graph optimization mechanism to refine the code representation, and apply an improved gated graph neural network to model variable-based flow graphs. To evaluate the effectiveness of deGraphCS, we collect a large-scale dataset from GitHub containing 41,152 code snippets written in C language, and reproduce several typical deep code search methods for comparison. Besides, we design a qualitative user study to verify the practical value of our approach. The experimental results have shown that deGraphCS can achieve state-of-the-art performances, and accurately retrieve code snippets satisfying the needs of the users.

We introduce GraphNet, a dataset of 2.7K real-world deep learning computational graphs with rich metadata, spanning six major task categories across multiple deep learning frameworks. To evaluate tensor compiler performance on these samples, we propose the benchmark metric Speedup Score S(t), which jointly considers runtime speedup and execution correctness under tunable tolerance levels, offering a reliable measure of general optimization capability. Furthermore, we extend S(t) to the Error-aware Speedup Score ES(t), which incorporates error information and helps compiler developers identify key performance bottlenecks. In this report, we benchmark the default tensor compilers, CINN for PaddlePaddle and TorchInductor for PyTorch, on computer vision (CV) and natural language processing (NLP) samples to demonstrate the practicality of GraphNet. The full construction pipeline with graph extraction and compiler evaluation tools is available at https://github.com/PaddlePaddle/GraphNet .

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared representation space using contrastive learning. However, systematic evaluations reveal significant performance degradation at structural boundaries where distinct topological patterns converge, with accuracy losses exceeding 20 percentage points. This issue arises from a key limitation: current methods assume all graph structures can be encoded within a single Euclidean space. In reality, tree structures require hyperbolic geometry to preserve hierarchical branching, while cyclic patterns depend on spherical geometry for closure properties. At structural boundaries, nodes experience conflicting geometric constraints that uniform encoding spaces cannot resolve. This raises a crucial challenge: Can alignment frameworks be designed to respect the intrinsic geometric diversity of graph structures? We introduce GraphShaper, a geometry-aware framework that enhances graph encoding through multi-geometric specialization. Our approach employs expert networks tailored to different geometric spaces, dynamically computing fusion weights to adaptively integrate geometric properties based on local structural characteristics. This adaptive fusion preserves structural integrity before alignment with text embeddings. Extensive experiments demonstrate that GraphShaper achieves 9.47\% accuracy improvements on citation networks and 7.63\% on social networks in zero-shot settings.

Although current Large Language Models (LLMs) exhibit impressive capabilities, performing complex real-world tasks still requires tool learning. Mainstream methods, such as CoT/ReAct, rely on step-by-step tool invocation to interact with external environments, but they are limited in perceptual scope and lack adequate task-planning capability. To address these limitations, other studies introduce the first Search-based Decision Tree (DFSDT), which still suffers from the high computational cost. In this paper, we introduce a novel parallel tool invocation paradigm, DTA-Llama (Divide-Then-Aggregate Llama). First, we transform traditional tree-based tool search paths into Directed Acyclic Graph (DAG) structure, generating a high-quality parallel tool invocation dataset. The DTA-Llama is then trained on the dataset to learn to iteratively divide the current task into several parallel tool invocation sub-tasks and aggregate the invocation results to decide the next actions. Furthermore, we introduce an efficient inference framework inspired by the Process/Threads mechanism when applying the DTA-Llama to practical tasks. Experimental results show that our approach substantially enhances task performance while reducing token consumption and inference time. Llama2-7B, using our method, is comparable to the official parallel function calling method of GPT-3.5. The relevant code, dataset, and model weights are available at https://corn0205.github.io/

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 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.

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.

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.

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

We propose a methodology that allows communication with Piping and Instrumentation Diagrams (P&IDs) using natural language. In particular, we represent P&IDs through the DEXPI data model as labeled property graphs and integrate them with Large Language Models (LLMs). The approach consists of three main parts: 1) P&IDs are cast into a graph representation from the DEXPI format using our pyDEXPI Python package. 2) A tool for generating P&ID knowledge graphs from pyDEXPI. 3) Integration of the P&ID knowledge graph to LLMs using graph-based retrieval augmented generation (graph-RAG). This approach allows users to communicate with P&IDs using natural language. It extends LLM's ability to retrieve contextual data from P&IDs and mitigate hallucinations. Leveraging the LLM's large corpus, the model is also able to interpret process information in PIDs, which could help engineers in their daily tasks. In the future, this work will also open up opportunities in the context of other generative Artificial Intelligence (genAI) solutions on P&IDs, and AI-assisted HAZOP studies.

Graph pre-training has achieved remarkable success in recent years, delivering transferable representations for downstream adaptation. However, most existing methods are designed for either homogeneous or heterogeneous graphs, thereby hindering unified graph modeling across diverse graph types. This separation contradicts real-world applications, where mixed homogeneous and heterogeneous graphs are ubiquitous, and distribution shifts between upstream pre-training and downstream deployment are common. In this paper, we empirically demonstrate that a balanced mixture of homogeneous and heterogeneous graph pre-training benefits downstream tasks and propose a unified multi-domain Graph Pre-training method across Homogeneous and Heterogeneous graphs (GPH^{2}). To address the lack of a unified encoder for homogeneous and heterogeneous graphs, we propose a Unified Multi-View Graph Construction that simultaneously encodes both without explicit graph-type-specific designs. To cope with the increased cross-domain distribution discrepancies arising from mixed graphs, we introduce domain-specific expert encoding. Each expert is independently pre-trained on a single graph to capture domain-specific knowledge, thereby shielding the pre-training encoder from the adverse effects of cross-domain discrepancies. For downstream tasks, we further design a Task-oriented Expert Fusion Strategy that adaptively integrates multiple experts based on their discriminative strengths. Extensive experiments on mixed graphs demonstrate that GPH^{2} enables stable transfer across graph types and domains, significantly outperforming existing graph pre-training methods.

This paper explores the transformative role of Agent AI and LangGraph in advancing the automation and effectiveness of machine translation (MT). Agents are modular components designed to perform specific tasks, such as translating between particular languages, with specializations like TranslateEnAgent, TranslateFrenchAgent, and TranslateJpAgent for English, French, and Japanese translations, respectively. These agents leverage the powerful semantic capabilities of large language models (LLMs), such as GPT-4o, to ensure accurate, contextually relevant translations while maintaining modularity, scalability, and context retention. LangGraph, a graph-based framework built on LangChain, simplifies the creation and management of these agents and their workflows. It supports dynamic state management, enabling agents to maintain dialogue context and automates complex workflows by linking agents and facilitating their collaboration. With flexibility, open-source community support, and seamless integration with LLMs, LangGraph empowers agents to deliver high-quality translations. Together, Agent AI and LangGraph create a cohesive system where LangGraph orchestrates agent interactions, ensuring that user inputs are analyzed, routed, and processed efficiently. Experimental results demonstrate the potential of this system to enhance multilingual translation accuracy and scalability. By highlighting modular design and automated workflows, this paper sets the stage for further innovations in intelligent machine translation services.

Large language models (LLMs) have demonstrated remarkable in-context reasoning capabilities across a wide range of tasks, particularly with unstructured inputs such as language or images. However, LLMs struggle to handle structured data, such as graphs, due to their lack of understanding of non-Euclidean structures. As a result, without additional fine-tuning, their performance significantly lags behind that of graph neural networks (GNNs) in graph learning tasks. In this paper, we show that learning on graph data can be conceptualized as a retrieval-augmented generation (RAG) process, where specific instances (e.g., nodes or edges) act as queries, and the graph itself serves as the retrieved context. Building on this insight, we propose a series of RAG frameworks to enhance the in-context learning capabilities of LLMs for graph learning tasks. Comprehensive evaluations demonstrate that our proposed RAG frameworks significantly improve LLM performance on graph-based tasks, particularly in scenarios where a pretrained LLM must be used without modification or accessed via an API.

Graph Retrieval-Augmented Generation (GraphRAG) enhances factual reasoning in LLMs by structurally modeling knowledge through graph-based representations. However, existing GraphRAG approaches face two core limitations: shallow retrieval that fails to surface all critical evidence, and inefficient utilization of pre-constructed structural graph data, which hinders effective reasoning from complex queries. To address these challenges, we propose GraphSearch, a novel agentic deep searching workflow with dual-channel retrieval for GraphRAG. GraphSearch organizes the retrieval process into a modular framework comprising six modules, enabling multi-turn interactions and iterative reasoning. Furthermore, GraphSearch adopts a dual-channel retrieval strategy that issues semantic queries over chunk-based text data and relational queries over structural graph data, enabling comprehensive utilization of both modalities and their complementary strengths. Experimental results across six multi-hop RAG benchmarks demonstrate that GraphSearch consistently improves answer accuracy and generation quality over the traditional strategy, confirming GraphSearch as a promising direction for advancing graph retrieval-augmented generation.

We present POTATO, a task- and languageindependent framework for human-in-the-loop (HITL) learning of rule-based text classifiers using graph-based features. POTATO handles any type of directed graph and supports parsing text into Abstract Meaning Representations (AMR), Universal Dependencies (UD), and 4lang semantic graphs. A streamlit-based user interface allows users to build rule systems from graph patterns, provides real-time evaluation based on ground truth data, and suggests rules by ranking graph features using interpretable machine learning models. Users can also provide patterns over graphs using regular expressions, and POTATO can recommend refinements of such rules. POTATO is applied in projects across domains and languages, including classification tasks on German legal text and English social media data. All components of our system are written in Python, can be installed via pip, and are released under an MIT License on GitHub.

Transformers for graph data are increasingly widely studied and successful in numerous learning tasks. Graph inductive biases are crucial for Graph Transformers, and previous works incorporate them using message-passing modules and/or positional encodings. However, Graph Transformers that use message-passing inherit known issues of message-passing, and differ significantly from Transformers used in other domains, thus making transfer of research advances more difficult. On the other hand, Graph Transformers without message-passing often perform poorly on smaller datasets, where inductive biases are more crucial. To bridge this gap, we propose the Graph Inductive bias Transformer (GRIT) -- a new Graph Transformer that incorporates graph inductive biases without using message passing. GRIT is based on several architectural changes that are each theoretically and empirically justified, including: learned relative positional encodings initialized with random walk probabilities, a flexible attention mechanism that updates node and node-pair representations, and injection of degree information in each layer. We prove that GRIT is expressive -- it can express shortest path distances and various graph propagation matrices. GRIT achieves state-of-the-art empirical performance across a variety of graph datasets, thus showing the power that Graph Transformers without message-passing can deliver.

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

The advancement of Large Language Models (LLMs) has remarkably pushed the boundaries towards artificial general intelligence (AGI), with their exceptional ability on understanding diverse types of information, including but not limited to images and audio. Despite this progress, a critical gap remains in empowering LLMs to proficiently understand and reason on graph data. Recent studies underscore LLMs' underwhelming performance on fundamental graph reasoning tasks. In this paper, we endeavor to unearth the obstacles that impede LLMs in graph reasoning, pinpointing the common practice of converting graphs into natural language descriptions (Graph2Text) as a fundamental bottleneck. To overcome this impediment, we introduce GraphLLM, a pioneering end-to-end approach that synergistically integrates graph learning models with LLMs. This synergy equips LLMs with the ability to proficiently interpret and reason on graph data, harnessing the superior expressive power of graph learning models. Our empirical evaluations across four fundamental graph reasoning tasks validate the effectiveness of GraphLLM. The results exhibit a substantial average accuracy enhancement of 54.44%, alongside a noteworthy context reduction of 96.45% across various graph reasoning tasks.

Tool-Augmented Language Models (TALMs) leverage external APIs to answer user queries across various domains. However, existing benchmark datasets for TALM research often feature simplistic dialogues that do not reflect real-world scenarios, such as the need for models to ask clarifying questions or proactively call additional APIs when essential information is missing. To address these limitations, we construct and release ToolDial, a dataset comprising 11,111 multi-turn dialogues, with an average of 8.95 turns per dialogue, based on APIs from RapidAPI. ToolDial has two key characteristics. First, the dialogues incorporate 16 user and system actions (e.g., "Request", "Clarify", "Fail inform") to capture the rich dynamics of real-world interactions. Second, we simulate dialogues where the system requests necessary information from the user based on API documentation and seeks additional APIs if the user fails to provide the required information. To facilitate this process, we introduce a method for generating an API graph that represents input and output compatibility between APIs. Using ToolDial, we evaluate a suite of language models on their ability to predict correct actions and extract input parameter values for API calls from the dialogue history. Modern language models achieve accuracy scores below 70%, indicating substantial room for improvement. We release our dataset and code at https://github.com/holi-lab/ToolDial.

Scene graph generation has emerged as a prominent research field in computer vision, witnessing significant advancements in the recent years. However, despite these strides, precise and thorough definitions for the metrics used to evaluate scene graph generation models are lacking. In this paper, we address this gap in the literature by providing a review and precise definition of commonly used metrics in scene graph generation. Our comprehensive examination clarifies the underlying principles of these metrics and can serve as a reference or introduction to scene graph metrics. Furthermore, to facilitate the usage of these metrics, we introduce a standalone Python package called SGBench that efficiently implements all defined metrics, ensuring their accessibility to the research community. Additionally, we present a scene graph benchmarking web service, that enables researchers to compare scene graph generation methods and increase visibility of new methods in a central place. All of our code can be found at https://lorjul.github.io/sgbench/.

Graph-based Retrieval-Augmented Generation (GraphRAG) organizes external knowledge as a hierarchical graph, enabling efficient retrieval and aggregation of scattered evidence across multiple documents. However, many existing benchmarks for GraphRAG rely on short, curated passages as external knowledge, failing to adequately evaluate systems in realistic settings involving long contexts and large-scale heterogeneous documents. To bridge this gap, we introduce WildGraphBench, a benchmark designed to assess GraphRAG performance in the wild. We leverage Wikipedia's unique structure, where cohesive narratives are grounded in long and heterogeneous external reference documents, to construct a benchmark reflecting real-word scenarios. Specifically, we sample articles across 12 top-level topics, using their external references as the retrieval corpus and citation-linked statements as ground truth, resulting in 1,100 questions spanning three levels of complexity: single-fact QA, multi-fact QA, and section-level summarization. Experiments across multiple baselines reveal that current GraphRAG pipelines help on multi-fact aggregation when evidence comes from a moderate number of sources, but this aggregation paradigm may overemphasize high-level statements at the expense of fine-grained details, leading to weaker performance on summarization tasks. Project page:https://github.com/BstWPY/WildGraphBench.

We introduceGraphGPT, a novel self-supervised generative pre-trained model for graph learning based on the Graph Eulerian Transformer (GET). First, we propose GET, which combines a standard transformer encoder or decoder architecture with an innovative graph-to-sequence transformation method. This method converts graphs or sampled subgraphs into sequences of tokens representing nodes, edges, and attributes in a reversible manner using Eulerian paths. We pre-train GET using either of the two self-supervised tasks: next-token prediction (NTP) and scheduled masked-token prediction (SMTP). The pre-trained model is then fine-tuned for downstream tasks such as graph-, edge-, and node-level prediction. Despite its simplicity, GraphGPT achieves performance comparable to or surpassing state-of-the-art methods on multiple large-scale Open Graph Benchmark (OGB) datasets. It demonstrates exceptional results on the molecular property prediction dataset PCQM4Mv2 and the protein-protein interaction dataset ogbl-ppa. Notably, generative pre-training enables scaling GraphGPT to 2 billion parameters while maintaining performance gains - a breakthrough that overcomes the scalability limitations of traditional Graph Neural Networks (GNNs) and prior graph transformers (GTs). To advance research in graph foundation models and facilitate scientific discovery in chemistry, materials science, and related fields, we will release the source code (https://github.com/alibaba/graph-gpt) and pre-trained checkpoints.

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.

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.

In recent years, graph pre-training has gained significant attention, focusing on acquiring transferable knowledge from unlabeled graph data to improve downstream performance. Despite these recent endeavors, the problem of negative transfer remains a major concern when utilizing graph pre-trained models to downstream tasks. Previous studies made great efforts on the issue of what to pre-train and how to pre-train by designing a variety of graph pre-training and fine-tuning strategies. However, there are cases where even the most advanced "pre-train and fine-tune" paradigms fail to yield distinct benefits. This paper introduces a generic framework W2PGNN to answer the crucial question of when to pre-train (i.e., in what situations could we take advantage of graph pre-training) before performing effortful pre-training or fine-tuning. We start from a new perspective to explore the complex generative mechanisms from the pre-training data to downstream data. In particular, W2PGNN first fits the pre-training data into graphon bases, each element of graphon basis (i.e., a graphon) identifies a fundamental transferable pattern shared by a collection of pre-training graphs. All convex combinations of graphon bases give rise to a generator space, from which graphs generated form the solution space for those downstream data that can benefit from pre-training. In this manner, the feasibility of pre-training can be quantified as the generation probability of the downstream data from any generator in the generator space. W2PGNN offers three broad applications: providing the application scope of graph pre-trained models, quantifying the feasibility of pre-training, and assistance in selecting pre-training data to enhance downstream performance. We provide a theoretically sound solution for the first application and extensive empirical justifications for the latter two applications.

Graph representations of programs are commonly a central element of machine learning for code research. We introduce an open source Python library python_graphs that applies static analysis to construct graph representations of Python programs suitable for training machine learning models. Our library admits the construction of control-flow graphs, data-flow graphs, and composite ``program graphs'' that combine control-flow, data-flow, syntactic, and lexical information about a program. We present the capabilities and limitations of the library, perform a case study applying the library to millions of competitive programming submissions, and showcase the library's utility for machine learning research.

Machine learning on graphs has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To solve this critical challenge, automated machine learning (AutoML) on graphs which combines the strength of graph machine learning and AutoML together, is gaining attention from the research community. Therefore, we comprehensively survey AutoML on graphs in this paper, primarily focusing on hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We further overview libraries related to automated graph machine learning and in-depth discuss AutoGL, the first dedicated open-source library for AutoML on graphs. In the end, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive review of automated machine learning on graphs to the best of our knowledge.

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

Retrieval-Augmented Generation (RAG) and Graph-based RAG has become the important paradigm for enhancing Large Language Models (LLMs) with external knowledge. However, existing approaches face a fundamental trade-off. While graph-based methods are inherently dependent on high-quality graph structures, they face significant practical constraints: manually constructed knowledge graphs are prohibitively expensive to scale, while automatically extracted graphs from corpora are limited by the performance of the underlying LLM extractors, especially when using smaller, local-deployed models. This paper presents Think-on-Graph 3.0 (ToG-3), a novel framework that introduces Multi-Agent Context Evolution and Retrieval (MACER) mechanism to overcome these limitations. Our core innovation is the dynamic construction and refinement of a Chunk-Triplets-Community heterogeneous graph index, which pioneeringly incorporates a dual-evolution mechanism of Evolving Query and Evolving Sub-Graph for precise evidence retrieval. This approach addresses a critical limitation of prior Graph-based RAG methods, which typically construct a static graph index in a single pass without adapting to the actual query. A multi-agent system, comprising Constructor, Retriever, Reflector, and Responser agents, collaboratively engages in an iterative process of evidence retrieval, answer generation, sufficiency reflection, and, crucially, evolving query and subgraph. This dual-evolving multi-agent system allows ToG-3 to adaptively build a targeted graph index during reasoning, mitigating the inherent drawbacks of static, one-time graph construction and enabling deep, precise reasoning even with lightweight LLMs. Extensive experiments demonstrate that ToG-3 outperforms compared baselines on both deep and broad reasoning benchmarks, and ablation studies confirm the efficacy of the components of MACER framework.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

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.

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being local, global or relative. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges O(N+E) by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework GraphGPS that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.

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/.

Large Language Models (LLMs) excel in stand-alone code tasks like HumanEval and MBPP, but struggle with handling entire code repositories. This challenge has prompted research on enhancing LLM-codebase interaction at a repository scale. Current solutions rely on similarity-based retrieval or manual tools and APIs, each with notable drawbacks. Similarity-based retrieval often has low recall in complex tasks, while manual tools and APIs are typically task-specific and require expert knowledge, reducing their generalizability across diverse code tasks and real-world applications. To mitigate these limitations, we introduce \framework, a system that integrates LLM agents with graph database interfaces extracted from code repositories. By leveraging the structural properties of graph databases and the flexibility of the graph query language, \framework enables the LLM agent to construct and execute queries, allowing for precise, code structure-aware context retrieval and code navigation. We assess \framework using three benchmarks: CrossCodeEval, SWE-bench, and EvoCodeBench. Additionally, we develop five real-world coding applications. With a unified graph database schema, \framework demonstrates competitive performance and potential in both academic and real-world environments, showcasing its versatility and efficacy in software engineering. Our application demo: https://github.com/modelscope/modelscope-agent/tree/master/apps/codexgraph_agent.

Large Language Models (LLMs) have garnered considerable interest within both academic and industrial. Yet, the application of LLMs to graph data remains under-explored. In this study, we evaluate the capabilities of four LLMs in addressing several analytical problems with graph data. We employ four distinct evaluation metrics: Comprehension, Correctness, Fidelity, and Rectification. Our results show that: 1) LLMs effectively comprehend graph data in natural language and reason with graph topology. 2) GPT models can generate logical and coherent results, outperforming alternatives in correctness. 3) All examined LLMs face challenges in structural reasoning, with techniques like zero-shot chain-of-thought and few-shot prompting showing diminished efficacy. 4) GPT models often produce erroneous answers in multi-answer tasks, raising concerns in fidelity. 5) GPT models exhibit elevated confidence in their outputs, potentially hindering their rectification capacities. Notably, GPT-4 has demonstrated the capacity to rectify responses from GPT-3.5-turbo and its own previous iterations. The code is available at: https://github.com/Ayame1006/LLMtoGraph.

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes the model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset.

Graph databases are gaining momentum thanks to the flexibility and expressiveness of their data models and query languages. A standardization activity driven by the ISO/IEC standardization body is also ongoing and has already conducted to the specification of the first versions of two standard graph query languages, namely SQL/PGQ and GQL, respectively in 2023 and 2024. Apart from the standards, there exists a panoply of concrete graph query languages provided by current graph database systems, each offering different query features. A common limitation of current graph query engines is the absence of an algebraic approach for evaluating path queries. To address this, we introduce an abstract algebra for evaluating path queries, allowing paths to be treated as first-class entities within the query processing pipeline. We demonstrate that our algebra can express a core fragment of path queries defined in GQL and SQL/PGQ, thereby serving as a formal framework for studying both standards and supporting their implementation in current graph database systems. We also show that evaluation trees for path algebra expressions can function as logical plans for evaluating path queries and enable the application of query optimization techniques. Our algebraic framework has the potential to act as a lingua franca for path query evaluation, enabling different implementations to be expressed and compared.

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.

Creating interactive scenes often involves complex programming tasks. Although large language models (LLMs) like ChatGPT can generate code from natural language, their output is often error-prone, particularly when scripting interactions among multiple elements. The linear conversational structure limits the editing of individual elements, and lacking graphical and precise control complicates visual integration. To address these issues, we integrate an element-level modularization technique that processes textual descriptions for individual elements through separate LLM modules, with a central module managing interactions among elements. This modular approach allows for refining each element independently. We design a graphical user interface, MoGraphGPT , which combines modular LLMs with enhanced graphical control to generate codes for 2D interactive scenes. It enables direct integration of graphical information and offers quick, precise control through automatically generated sliders. Our comparative evaluation against an AI coding tool, Cursor Composer, as the baseline system and a usability study show MoGraphGPT significantly improves easiness, controllability, and refinement in creating complex 2D interactive scenes with multiple visual elements in a coding-free manner.

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.

Following the success of Word2Vec embeddings, graph embeddings (GEs) have gained substantial traction. GEs are commonly generated and evaluated extrinsically on downstream applications, but intrinsic evaluations of the original graph properties in terms of topological structure and semantic information have been lacking. Understanding these will help identify the deficiency of the various families of GE methods when vectorizing graphs in terms of preserving the relevant knowledge or learning incorrect knowledge. To address this, we propose RESTORE, a framework for intrinsic GEs assessment through graph reconstruction. We show that reconstructing the original graph from the underlying GEs yields insights into the relative amount of information preserved in a given vector form. We first introduce the graph reconstruction task. We generate GEs from three GE families based on factorization methods, random walks, and deep learning (with representative algorithms from each family) on the CommonSense Knowledge Graph (CSKG). We analyze their effectiveness in preserving the (a) topological structure of node-level graph reconstruction with an increasing number of hops and (b) semantic information on various word semantic and analogy tests. Our evaluations show deep learning-based GE algorithm (SDNE) is overall better at preserving (a) with a mean average precision (mAP) of 0.54 and 0.35 for 2 and 3-hop reconstruction respectively, while the factorization-based algorithm (HOPE) is better at encapsulating (b) with an average Euclidean distance of 0.14, 0.17, and 0.11 for 1, 2, and 3-hop reconstruction respectively. The modest performance of these GEs leaves room for further research avenues on better graph representation learning.

Large language model-based (LLM-based) multi-agent systems (MAS) are increasingly used to extend agentic problem solving via role specialization and collaboration. MAS workflows can be naturally modeled as directed computation graphs, where nodes execute agents/sub-workflows and edges encode dependencies and message passing. However, implementing complex graph workflows in current frameworks still requires substantial manual effort, offers limited reuse, and makes it difficult to integrate heterogeneous external context sources. To overcome these limitations, we present MASFactory, a graph-centric framework for orchestrating LLM-based MAS. It introduces Vibe Graphing, a human-in-the-loop approach that compiles natural-language intent into an editable workflow specification and then into an executable graph. In addition, the framework provides reusable components and pluggable context integration, as well as a visualizer for topology preview, runtime tracing, and human-in-the-loop interaction. We evaluate MASFactory on seven public benchmarks, validating both reproduction consistency for representative MAS methods and the effectiveness of Vibe Graphing. Our code (https://github.com/BUPT-GAMMA/MASFactory) and video (https://youtu.be/ANynzVfY32k) are publicly available.

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.

Large language models (LLMs) have achieved impressive success across several fields, but their proficiency in understanding and resolving complex graph problems is less explored. To bridge this gap, we introduce GraphInstruct, a novel and comprehensive instruction-tuning dataset designed to equip language models with the ability to tackle a broad spectrum of graph problems using explicit reasoning paths. Utilizing GraphInstruct, we build GraphWiz, an open-source language model capable of resolving various graph problem types while generating clear reasoning processes. To enhance the model's capability and reliability, we incorporate the Direct Preference Optimization (DPO) framework into the graph problem-solving context. The enhanced model, GraphWiz-DPO, achieves an average accuracy of 65% across nine tasks with different complexity levels, surpassing GPT-4 which has an average accuracy of 43.8%. Moreover, our research delves into the delicate balance between training data volume and model performance, highlighting the potential for overfitting with increased data. We also explore the transferability of the model's reasoning ability across different graph tasks, indicating the model's adaptability and practical application potential. Our investigation offers a new blueprint and valuable insights for developing LLMs specialized in graph reasoning and problem-solving.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

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}

Graph Neural Networks (GNNs) are popular models for graph learning problems. GNNs show strong empirical performance in many practical tasks. However, the theoretical properties have not been completely elucidated. In this paper, we investigate whether GNNs can exploit the graph structure from the perspective of the expressive power of GNNs. In our analysis, we consider graph generation processes that are controlled by hidden (or latent) node features, which contain all information about the graph structure. A typical example of this framework is kNN graphs constructed from the hidden features. In our main results, we show that GNNs can recover the hidden node features from the input graph alone, even when all node features, including the hidden features themselves and any indirect hints, are unavailable. GNNs can further use the recovered node features for downstream tasks. These results show that GNNs can fully exploit the graph structure by themselves, and in effect, GNNs can use both the hidden and explicit node features for downstream tasks. In the experiments, we confirm the validity of our results by showing that GNNs can accurately recover the hidden features using a GNN architecture built based on our theoretical analysis.

Tool-augmented large language models (LLMs) are attracting widespread attention when accessing up-to-date knowledge and alleviating hallucination issues. Nowadays, advanced closed-source LLMs (e.g., ChatGPT) have demonstrated surprising tool-usage capabilities through prompting and in-context learning techniques. To empower the capabilities of open-source LLMs (e.g., LLaMA) in manipulating tools, current efforts focus on either template-driven or token-triggered tool-usage. However, the former hampers LLMs' flexibility to address diverse user's queries due to constrained tool interactions, while the latter limits the generalizability when engaging with new tools, since tool-usage learning is based on task- and tool-specific datasets. To alleviate these concerns, in this paper, we propose a decision-aware and generalizable tool-usage framework (DEER). Specifically, we first construct the tool-usage samples with multiple decision branches via an automatic generation pipeline, thereby inspiring the decision-making awareness of LLMs under diverse scenarios. Meanwhile, we propose a novel tool sampling strategy to enhance the generalizability of LLMs over unseen tools. Extensive experiments demonstrate that our proposed DEER is effective and significantly outperforms baselines across various datasets.

Knowledge graphs are useful tools to organize, recommend and sort data. Hierarchies in knowledge graphs provide significant benefit in improving understanding and compartmentalization of the data within a knowledge graph. This work leverages large language models to generate and augment hierarchies in an existing knowledge graph. For small (<100,000 node) domain-specific KGs, we find that a combination of few-shot prompting with one-shot generation works well, while larger KG may require cyclical generation. We present techniques for augmenting hierarchies, which led to coverage increase by 98% for intents and 99% for colors in our knowledge graph.

The issue localization task aims to identify the locations in a software repository that requires modification given a natural language issue description. This task is fundamental yet challenging in automated software engineering due to the semantic gap between issue description and source code implementation. This gap manifests as two mismatches:(1) symptom-to-cause mismatches, where descriptions do not explicitly reveal underlying root causes; (2) one-to-many mismatches, where a single issue corresponds to multiple interdependent code entities. To address these two mismatches, we propose GraphLocator, an approach that mitigates symptom-to-cause mismatches through causal structure discovering and resolves one-to-many mismatches via dynamic issue disentangling. The key artifact is the causal issue graph (CIG), in which vertices represent discovered sub-issues along with their associated code entities, and edges encode the causal dependencies between them. The workflow of GraphLocator consists of two phases: symptom vertices locating and dynamic CIG discovering; it first identifies symptom locations on the repository graph, then dynamically expands the CIG by iteratively reasoning over neighboring vertices. Experiments on three real-world datasets demonstrates the effectiveness of GraphLocator: (1) Compared with baselines, GraphLocator achieves more accurate localization with average improvements of +19.49% in function-level recall and +11.89% in precision. (2) GraphLocator outperforms baselines on both symptom-to-cause and one-to-many mismatch scenarios, achieving recall improvement of +16.44% and +19.18%, precision improvement of +7.78% and +13.23%, respectively. (3) The CIG generated by GraphLocator yields the highest relative improvement, resulting in a 28.74% increase in performance on downstream resolving task.

External tool integration through function-calling is essential for practical language model applications, yet most multilingual models lack reliable tool-use capabilities in non-English languages. Even state-of-the-art multilingual models struggle with determining when to use tools and generating the structured outputs required for function calls, often exhibiting language confusion when prompted in lower-resource languages. This work presents a methodology for adapting existing language models to enable robust tool use in any target language, using Bulgarian as a case study. The approach involves continued training of the BgGPT model series (2.6B, 9B, 27B parameters) on a novel bilingual dataset of 10,035 function-calling examples designed to support standardized protocols like MCP (Model Context Protocol). The research introduces TUCAN (Tool-Using Capable Assistant Navigator), which achieves up to 28.75% improvement in function-calling accuracy over base models while preserving core language understanding, as verified on established Bulgarian benchmarks. Beyond accuracy gains, TUCAN models demonstrate production-ready response formatting with clean, parsable function calls, contrasting with the verbose and inconsistent outputs of base models. The models, evaluation framework, and dataset are released to enable replication for other languages. This work demonstrates a practical approach for extending tool-augmented capabilities beyond English-centric systems.

Despite the prevalence of recent success in learning from static graphs, learning from time-evolving graphs remains an open challenge. In this work, we design new, more stringent evaluation procedures for link prediction specific to dynamic graphs, which reflect real-world considerations, to better compare the strengths and weaknesses of methods. First, we create two visualization techniques to understand the reoccurring patterns of edges over time and show that many edges reoccur at later time steps. Based on this observation, we propose a pure memorization baseline called EdgeBank. EdgeBank achieves surprisingly strong performance across multiple settings because easy negative edges are often used in the current evaluation setting. To evaluate against more difficult negative edges, we introduce two more challenging negative sampling strategies that improve robustness and better match real-world applications. Lastly, we introduce six new dynamic graph datasets from a diverse set of domains missing from current benchmarks, providing new challenges and opportunities for future research. Our code repository is accessible at https://github.com/fpour/DGB.git.

Multi-domain graph pre-training integrates knowledge from diverse domains to enhance performance in the target domains, which is crucial for building graph foundation models. Despite initial success, existing solutions often fall short of answering a fundamental question: how is knowledge integrated or transferred across domains? This theoretical limitation motivates us to rethink the consistency and transferability between model pre-training and domain adaptation. In this paper, we propose a fresh Riemannian geometry perspective, whose core idea is to merge any graph dataset into a unified, smooth Riemannian manifold, enabling a systematic understanding of knowledge integration and transfer. To achieve this, our key contribution is the theoretical establishment of neural manifold gluing, which first characterizes local geometry using an adaptive orthogonal frame and then "glues" the local pieces together into a coherent whole. Building on this theory, we present the GraphGlue framework, which supports batched pre-training with EMA prototyping and provides a transferability measure based on geometric consistence. Extensive experiments demonstrate its superior performance across diverse graph domains. Moreover, we empirically validated GraphGlue's geometric scaling law, showing that larger quantities of datasets improve model transferability by producing a smoother manifold. Codes are available at https://github.com/RiemannGraph/GraphGlue.

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.

In this paper, we presented GraphOmni, a comprehensive benchmark framework for systematically evaluating the graph reasoning capabilities of LLMs. By analyzing critical dimensions, including graph types, serialization formats, and prompt schemes, we provided extensive insights into the strengths and limitations of current LLMs. Our empirical findings emphasize that no single serialization or prompting strategy consistently outperforms others. Motivated by these insights, we propose a reinforcement learning-based approach that dynamically selects the best serialization-prompt pairings, resulting in significant accuracy improvements. GraphOmni's modular and extensible design establishes a robust foundation for future research, facilitating advancements toward general-purpose graph reasoning models.