Daily Papers

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.

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

Tool agents--LLM-based systems that interact with external APIs--offer a way to execute real-world tasks. However, as tasks become increasingly complex, these agents struggle to identify and call the correct APIs in the proper order. To tackle this problem, we investigate converting API documentation into a structured API graph that captures API dependencies and leveraging it for multi-tool queries that require compositional API calls. To support this, we introduce In-N-Out, the first expert-annotated dataset of API graphs built from two real-world API benchmarks and their documentation. Using In-N-Out significantly improves performance on both tool retrieval and multi-tool query generation, nearly doubling that of LLMs using documentation alone. Moreover, graphs generated by models fine-tuned on In-N-Out close 90% of this gap, showing that our dataset helps models learn to comprehend API documentation and parameter relationships. Our findings highlight the promise of using explicit API graphs for tool agents and the utility of In-N-Out as a valuable resource. We release our dataset and code at https://github.com/holi-lab/In-N-Out-API-Graph.

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.

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}}.}.

The rapid capability gains of frontier language models are widely attributed to improved reasoning abilities, yet this cannot be verified as raw CoT traces in closed-source systems are hidden. By registering a simple custom tool through a standard API feature, we induce frontier models to externalize intermediate reasoning. Because these traces may reflect post-hoc rationalization rather than genuine reasoning, we first evaluate against native CoT on open-source models and extend to closed-source frontier models including GPT-6 Astra. We find that the extracted reasoning matches native reasoning performance and substantially outperforms no-reasoning baselines, across competition mathematics, science, and code generation. We then characterize how frontier models structure their intermediate reasoning. Across token efficiency, reasoning-step types, and induced reasoning trees, we identify systematic differences in how models externalize, compress, and organize reasoning. We find that Astra exhibits token-efficient directed reasoning, selecting a correct trajectory earlier, while resolving elementary steps internally and externalizing only crucial reasoning. These findings provide a behavioral lens on frontier-model reasoning beyond benchmark scores.

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.

Large Language Models (LLMs) reasoning processes are challenging to analyze due to their complexity and the lack of organized visualization tools. We present ReasonGraph, a web-based platform for visualizing and analyzing LLM reasoning processes. It supports both sequential and tree-based reasoning methods while integrating with major LLM providers and over fifty state-of-the-art models. ReasonGraph incorporates an intuitive UI with meta reasoning method selection, configurable visualization parameters, and a modular framework that facilitates efficient extension. Our evaluation shows high parsing reliability, efficient processing, and strong usability across various downstream applications. By providing a unified visualization framework, ReasonGraph reduces cognitive load in analyzing complex reasoning paths, improves error detection in logical processes, and enables more effective development of LLM-based applications. The platform is open-source, promoting accessibility and reproducibility in LLM reasoning analysis.

Graph Retrieval Augmented Generation (GraphRAG) effectively enhances external knowledge integration capabilities by explicitly modeling knowledge relationships, thereby improving the factual accuracy and generation quality of Large Language Models (LLMs) in specialized domains. However, existing methods suffer from two inherent limitations: 1) Inefficient Information Aggregation: They rely on a single agent and fixed iterative patterns, making it difficult to adaptively capture multi-level textual, structural, and degree information within graph data. 2) Rigid Reasoning Mechanism: They employ preset reasoning schemes, which cannot dynamically adjust reasoning depth nor achieve precise semantic correction. To overcome these limitations, we propose Graph Counselor, an GraphRAG method based on multi-agent collaboration. This method uses the Adaptive Graph Information Extraction Module (AGIEM), where Planning, Thought, and Execution Agents work together to precisely model complex graph structures and dynamically adjust information extraction strategies, addressing the challenges of multi-level dependency modeling and adaptive reasoning depth. Additionally, the Self-Reflection with Multiple Perspectives (SR) module improves the accuracy and semantic consistency of reasoning results through self-reflection and backward reasoning mechanisms. Experiments demonstrate that Graph Counselor outperforms existing methods in multiple graph reasoning tasks, exhibiting higher reasoning accuracy and generalization ability. Our code is available at https://github.com/gjq100/Graph-Counselor.git.

Large Language Models (LLMs) show strong reasoning ability in open-domain question answering, yet their reasoning processes are typically linear and often logically inconsistent. In contrast, real-world reasoning requires integrating multiple premises and solving subproblems in parallel. Existing methods, such as Chain-of-Thought (CoT), express reasoning in a linear textual form, which may appear coherent but frequently leads to inconsistent conclusions. Recent approaches rely on externally provided graphs and do not explore how LLMs can construct and use their own graph-structured reasoning, particularly in open-domain QA. To fill this gap, we novelly explore graph-structured reasoning of LLMs in general-domain question answering. We propose Self-Graph Reasoning (SGR), a framework that enables LLMs to explicitly represent their reasoning process as a structured graph before producing the final answer. We further construct a graph-structured reasoning dataset that merges multiple candidate reasoning graphs into refined graph structures for model training. Experiments on five QA benchmarks across both general and specialized domains show that SGR consistently improves reasoning consistency and yields a 17.74% gain over the base model. The LLaMA-3.3-70B model fine-tuned with SGR performs comparably to GPT-4o and surpasses Claude-3.5-Haiku, demonstrating the effectiveness of graph-structured reasoning.

Large Language Models (LLMs) have showcased impressive reasoning capabilities, particularly when guided by specifically designed prompts in complex reasoning tasks such as math word problems. These models typically solve tasks using a chain-of-thought approach, which not only bolsters their reasoning abilities but also provides valuable insights into their problem-solving process. However, there is still significant room for enhancing the reasoning abilities of LLMs. Some studies suggest that the integration of an LLM output verifier can boost reasoning accuracy without necessitating additional model training. In this paper, we follow these studies and introduce a novel graph-based method to further augment the reasoning capabilities of LLMs. We posit that multiple solutions to a reasoning task, generated by an LLM, can be represented as a reasoning graph due to the logical connections between intermediate steps from different reasoning paths. Therefore, we propose the Reasoning Graph Verifier (RGV) to analyze and verify the solutions generated by LLMs. By evaluating these graphs, models can yield more accurate and reliable results.Our experimental results show that our graph-based verification method not only significantly enhances the reasoning abilities of LLMs but also outperforms existing verifier methods in terms of improving these models' reasoning performance.

Graph embedding methods such as Graph Neural Networks (GNNs) and Graph Transformers have contributed to the development of graph reasoning algorithms for various tasks on knowledge graphs. However, the lack of interpretability and explainability of graph embedding methods has limited their applicability in scenarios requiring explicit reasoning. In this paper, we introduce the Graph Agent (GA), an intelligent agent methodology of leveraging large language models (LLMs), inductive-deductive reasoning modules, and long-term memory for knowledge graph reasoning tasks. GA integrates aspects of symbolic reasoning and existing graph embedding methods to provide an innovative approach for complex graph reasoning tasks. By converting graph structures into textual data, GA enables LLMs to process, reason, and provide predictions alongside human-interpretable explanations. The effectiveness of the GA was evaluated on node classification and link prediction tasks. Results showed that GA reached state-of-the-art performance, demonstrating accuracy of 90.65%, 95.48%, and 89.32% on Cora, PubMed, and PrimeKG datasets, respectively. Compared to existing GNN and transformer models, GA offered advantages of explicit reasoning ability, free-of-training, easy adaption to various graph reasoning tasks

Large language models (LLMs) augmented with tools are emerging as autonomous agents capable of using Web engine, APIs, and code to solve complex, long-horizon tasks. Current tool-using benchmarks for information seeking on academic graphs rely on synthetic templates, simplified solution spaces, or narrow tasks such as paper-centric tasks, leaving key challenges underexplored - realistic user intent, complex multi-step API planning, rich parameter filling for APIs, grounded answers with references, and comprehensive evaluation of both the process and the outcome. We introduce AISE-Bench, a real-world, full-cycle annotated benchmark for information seeking on academic knowledge graphs. AISE-Bench release contains 1,133 QA pairs, including query taxonomies, full API execution trajectories, validated parameters, and source-grounded answers with reference links. To support high-quality annotation, we design a customized agent workflow to enable annotators to plan, execute, and revise complex API workflows efficiently. We develop a comprehensive evaluation protocol measuring answer quality, reference grounding, API-planning correctness, and execution success. Among the 14 evaluated methods, even the strongest model (PLAY2PROMPT with Gemini-3-Pro) achieves only moderate performance and often struggles with API planning and execution. AISE-Bench establishes a challenging new testbed for quantitatively evaluating and improving the stepwise correctness, grounded summarization, and traceable reasoning of multi-step API-using LLM agents. Our code and data are available at https://aise-bench.github.io/.

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.

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

Recent advances in search-augmented large reasoning models (LRMs) enable the retrieval of external knowledge to reduce hallucinations in multistep reasoning. However, their ability to operate on graph-structured data, prevalent in domains such as e-commerce, social networks, and scientific citations, remains underexplored. Unlike plain text corpora, graphs encode rich topological signals that connect related entities and can serve as valuable priors for retrieval, enabling more targeted search and improved reasoning efficiency. Yet, effectively leveraging such structure poses unique challenges, including the difficulty of generating graph-expressive queries and ensuring reliable retrieval that balances structural and semantic relevance. To address this gap, we introduce GraphSearch, the first framework that extends search-augmented reasoning to graph learning, enabling zero-shot graph learning without task-specific fine-tuning. GraphSearch combines a Graph-aware Query Planner, which disentangles search space (e.g., 1-hop, multi-hop, or global neighbors) from semantic queries, with a Graph-aware Retriever, which constructs candidate sets based on topology and ranks them using a hybrid scoring function. We further instantiate two traversal modes: GraphSearch-R, which recursively expands neighborhoods hop by hop, and GraphSearch-F, which flexibly retrieves across local and global neighborhoods without hop constraints. Extensive experiments across diverse benchmarks show that GraphSearch achieves competitive or even superior performance compared to supervised graph learning methods, setting state-of-the-art results in zero-shot node classification and link prediction. These findings position GraphSearch as a flexible and generalizable paradigm for agentic reasoning over graphs.

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.

To achieve faithful reasoning that aligns with human expectations, large language models (LLMs) need to ground their reasoning to real-world knowledge (e.g., web facts, math and physical rules). Tools help LLMs access this external knowledge, but there remains challenges for fine-tuning LLM agents (e.g., Toolformer) to invoke tools in multi-step reasoning problems, where inter-connected tool calls require holistic and efficient tool usage planning. In this work, we propose a new method for LLMs to better leverage tools in multi-step reasoning. Our method, Chain-of-Abstraction (CoA), trains LLMs to first decode reasoning chains with abstract placeholders, and then call domain tools to reify each reasoning chain by filling in specific knowledge. This planning with abstract chains enables LLMs to learn more general reasoning strategies, which are robust to shifts of domain knowledge (e.g., math results) relevant to different reasoning questions. It also allows LLMs to perform decoding and calling of external tools in parallel, which avoids the inference delay caused by waiting for tool responses. In mathematical reasoning and Wiki QA domains, we show that our method consistently outperforms previous chain-of-thought and tool-augmented baselines on both in-distribution and out-of-distribution test sets, with an average ~6% absolute QA accuracy improvement. LLM agents trained with our method also show more efficient tool use, with inference speed being on average ~1.4x faster than baseline tool-augmented LLMs.

Large Language Models (LLMs) have made remarkable strides in reasoning tasks, yet their performance often falters on novel and complex problems. Domain-specific continued pretraining (CPT) methods, such as those tailored for mathematical reasoning, have shown promise but lack transferability to broader reasoning tasks. In this work, we pioneer the use of Graph Problem Reasoning (GPR) to enhance the general reasoning capabilities of LLMs. GPR tasks, spanning pathfinding, network analysis, numerical computation, and topological reasoning, require sophisticated logical and relational reasoning, making them ideal for teaching diverse reasoning patterns. To achieve this, we introduce GraphPile, the first large-scale corpus specifically designed for CPT using GPR data. Spanning 10.9 billion tokens across 23 graph tasks, the dataset includes chain-of-thought, program-of-thought, trace of execution, and real-world graph data. Using GraphPile, we train GraphMind on popular base models Llama 3 and 3.1, as well as Gemma 2, achieving up to 4.9 percent higher accuracy in mathematical reasoning and up to 21.2 percent improvement in non-mathematical reasoning tasks such as logical and commonsense reasoning. By being the first to harness GPR for enhancing reasoning patterns and introducing the first dataset of its kind, our work bridges the gap between domain-specific pretraining and universal reasoning capabilities, advancing the adaptability and robustness of LLMs.

Large language models (LLMs) excel at complex reasoning but remain limited by static and incomplete parametric knowledge. Retrieval-augmented generation (RAG) mitigates this by incorporating external knowledge, yet existing RAGs struggle with knowledge-intensive tasks due to fragmented information and weak modeling of knowledge structure. Graphs offer a natural way to model relationships within knowledge, but LLMs are inherently unstructured and cannot effectively reason over graph-structured data. Recent graph-enhanced RAG (GraphRAG) attempts to bridge this gap by constructing tailored graphs and enabling LLMs to reason on them. However, these methods often depend on ad-hoc graph designs, heuristic search, or costly agent pipelines, which hinder scalability and generalization. To address these challenges, we present G-reasoner, a unified framework that integrates graph and language foundation models for scalable reasoning over diverse graph-structured knowledge. Central to our approach is QuadGraph, a standardized four-layer abstraction that unifies heterogeneous knowledge sources into a common graph representation. Building on this, we introduce a 34M-parameter graph foundation model (GFM) that jointly captures graph topology and textual semantics, and is integrated with LLMs to enhance reasoning in downstream applications. To ensure scalability and efficiency, mixed-precision training and distributed message-passing are implemented to scale GFM with more GPUs. Extensive experiments on six benchmarks show that G-reasoner consistently outperforms state-of-the-art baselines, significantly enhances LLM reasoning, and achieves strong efficiency and cross-graph generalization.

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.

We introduce ARBIGRAPH, a benchmark generator for evaluating whether tool-assisted language agents can retain, update, compose, and discard task-relevant context across extended reasoning workflows. ARBIGRAPH represents each task as a natural-language problem with an executable Python solver, and composes tasks through typed intermediate states, instantiated here as scalar and list values. This design enables controllable task graphs whose length, dependency structure, distractor count, and value type can be varied while preserving exact automatic verification. We instantiate ARBIGRAPH with math, GSM-style word-problems, and Python-tracing task categories, and evaluate a Qwen3.5-27B tool-assisted agent across four topologies. The results show high accuracy on isolated tasks but substantial degradation on more complex dependent tasks: accuracy drops by up to 33.3% on branching chains of dependent math tasks. This shows that ARBIGRAPH exposes failures that are not visible from single-task evaluation alone. Our code, generated datasets, and evaluation results are available at https://github.com/pavelgolikov/ArbiGraph.git

Graph Retrieval-Augmented Generation (GraphRAG) is dominated by a retrieve-then-reason paradigm, where context is retrieved using heuristics and then reasoned over. Such methods struggle to adapt to the query-specific logic required for complex multi-hop tasks, often accumulating irrelevant context or missing correct relational paths. We propose DotRAG, a training-free GraphRAG framework that reformulates retrieval as a reasoning process over paths. Our approach generates query-conditioned constraints that guide graph exploration, prune irrelevant regions, and iteratively discover relational paths without relying on explicit step-by-step reasoning chains. We introduce Division of Thought (DOT), an abstraction that decomposes retrieval into localized search spaces and adapts the search strategy to each query. DotRAG achieves SOTA performance on MetaQA and UltraDomain, with consistent gains on multi-hop tasks, demonstrating the effectiveness of reasoning-guided retrieval.

Although large language models (LLMs) have achieved significant success in various tasks, they often struggle with hallucination problems, especially in scenarios requiring deep and responsible reasoning. These issues could be partially addressed by introducing external knowledge graphs (KG) in LLM reasoning. In this paper, we propose a new LLM-KG integrating paradigm ``LLMotimesKG'' which treats the LLM as an agent to interactively explore related entities and relations on KGs and perform reasoning based on the retrieved knowledge. We further implement this paradigm by introducing a new approach called Think-on-Graph (ToG), in which the LLM agent iteratively executes beam search on KG, discovers the most promising reasoning paths, and returns the most likely reasoning results. We use a number of well-designed experiments to examine and illustrate the following advantages of ToG: 1) compared with LLMs, ToG has better deep reasoning power; 2) ToG has the ability of knowledge traceability and knowledge correctability by leveraging LLMs reasoning and expert feedback; 3) ToG provides a flexible plug-and-play framework for different LLMs, KGs and prompting strategies without any additional training cost; 4) the performance of ToG with small LLM models could exceed large LLM such as GPT-4 in certain scenarios and this reduces the cost of LLM deployment and application. As a training-free method with lower computational cost and better generality, ToG achieves overall SOTA in 6 out of 9 datasets where most previous SOTAs rely on additional training.

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.

Large language models have shown strong performance in natural language generation and downstream reasoning tasks, but they still struggle with logical consistency, factual grounding, and interpretability in complex multi-step reasoning. To address these limitations, this paper proposes SGR, a stepwise reasoning enhancement framework that integrates large language models with external knowledge graphs through query-relevant subgraph generation. Given an input question, SGR first extracts key entities, relations, and constraints to construct a structured schema, then retrieves compact subgraphs from a knowledge graph using schema-guided querying. The generated subgraphs provide explicit relational evidence that guides the language model through step-by-step reasoning. In addition, SGR combines direct Cypher-based reasoning with collaborative reasoning integration, allowing candidate answers from multiple reasoning paths to be validated and aggregated according to both model confidence and graph consistency. Experiments on benchmark datasets including CWQ, WebQSP, GrailQA, and KQA Pro demonstrate that SGR improves reasoning accuracy and Hits@1 performance over standard prompting and several knowledge-enhanced baselines. Ablation studies further show that schema guidance and Neo4j-based retrieval are both crucial to the effectiveness of the framework. These results indicate that dynamically generated external subgraphs can improve the accuracy, robustness, and interpretability of LLM-based reasoning.

The generation of explanation graphs is a significant task that aims to produce explanation graphs in response to user input, revealing the internal reasoning process. This task is challenging due to the significant discrepancy between unstructured user queries and structured explanation graphs. Current research commonly fine-tunes a text-based pre-trained language model on a small downstream dataset that is annotated with labeled graphs. However, due to the limited scale of available datasets, this approach may prove to be insufficient in bridging the gap between natural language text and structured graphs. In this paper, to alleviate the above limitations, we propose a novel pre-trained framework EG3P(for Explanation Graph Generation via Generative Pre-training over synthetic graphs) for the explanation graph generation task. Specifically, we first propose a text-to-graph generative task to pre-train the model with the goal of bridging the text-graph gap. Additionally, we propose an automatic corpus synthesis strategy for synthesizing a large scale of high-quality corpus, reducing the reliance on costly manual annotation methods. Experimental results on ExplaGraphs show the effectiveness of EG3P that our model surpasses all baseline systems with remarkable margins. Besides, further analysis demonstrates that EG3P is able to generate better explanation graphs on actual reasoning tasks such as CommonsenseQA and OpenbookQA.

Large language models (LLMs) are increasingly used to complete complex tasks by selecting and coordinating external tools across multiple steps. This requires aligning tool choices with subtask intent while satisfying directional execution dependencies among tools. To do this, existing methods model these dependencies as tool graphs and incorporate the graphs with LLMs through retrieval, serialization, or prompt-level injection. However, these external graph-use strategies all follow a matching paradigm, which often fails to align tool choices with the underlying subtask structure, producing semantically plausible plans that violate graph constraints. This issue is further exacerbated by error accumulation, where an early incorrect tool selection shifts the plan into an invalid graph state and causes subsequent predictions to drift away from the valid execution path. To address these challenges, we propose GRAFT, a graph-tokenized language model framework for dependency-aware tool planning. GRAFT internalizes the tool graph by mapping each tool node to a dedicated special token and learning directed tool dependencies within the representation space. It further introduces on-policy tool context distillation, training the model on its own sampled trajectories while distilling stepwise planning signals. Experiments show that GRAFT achieves state-of-the-art performance in exact sequence matching and dependency legality, supporting more reliable LLM tool planning in complex workflows.

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.

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.

Knowledge Graphs (KGs) are valuable tools for representing relationships between entities in a structured format. Traditionally, these knowledge bases are queried to extract specific information. However, question-answering (QA) over such KGs poses a challenge due to the intrinsic complexity of natural language compared to the structured format and the size of these graphs. Despite these challenges, the structured nature of KGs can provide a solid foundation for grounding the outputs of Large Language Models (LLMs), offering organizations increased reliability and control. Recent advancements in LLMs have introduced reasoning methods at inference time to improve their performance and maximize their capabilities. In this work, we propose integrating these reasoning strategies with KGs to anchor every step or "thought" of the reasoning chains in KG data. Specifically, we evaluate both agentic and automated search methods across several reasoning strategies, including Chain-of-Thought (CoT), Tree-of-Thought (ToT), and Graph-of-Thought (GoT), using GRBench, a benchmark dataset for graph reasoning with domain-specific graphs. Our experiments demonstrate that this approach consistently outperforms baseline models, highlighting the benefits of grounding LLM reasoning processes in structured KG data.

Graph RAG mitigates hallucinations and stale knowledge in LLMs, particularly for multi-hop question answering. However, existing approaches remain highly fragmented and incompatible. The structural heterogeneity of graph formats across different frameworks and the lack of granular visualization tools make it exceedingly difficult to evaluate and compare retrieval behaviors. To bridge this gap, we propose GraphContainer, a novel platform designed to unify and visualize diverse graph RAG workflows. GraphContainer features two key components: (1) a Unified Graph Representation (UGR) layer that seamlessly standardizes multi-format graphs, and (2) a Graph Recorder that tracks and visually renders the step-by-step retrieval process. Through an interactive web interface, we demonstrate GraphContainer's ability to import heterogeneous graphs and perform live, traceable visual debugging of graph RAG methods. Ultimately, we show how GraphContainer enables controlled comparisons of various graph formats and retrieval strategies, lowering the barrier for researchers and practitioners to design optimal graph RAG pipelines. A demonstration video is available at https://youtu.be/O02eNJLwkU0.

Large language models (LLMs) can perform complex reasoning in few- and zero-shot settings by generating intermediate chain of thought (CoT) reasoning steps. Further, each reasoning step can rely on external tools to support computation beyond the core LLM capabilities (e.g. search/running code). Prior work on CoT prompting and tool use typically requires hand-crafting task-specific demonstrations and carefully scripted interleaving of model generations with tool use. We introduce Automatic Reasoning and Tool-use (ART), a framework that uses frozen LLMs to automatically generate intermediate reasoning steps as a program. Given a new task to solve, ART selects demonstrations of multi-step reasoning and tool use from a task library. At test time, ART seamlessly pauses generation whenever external tools are called, and integrates their output before resuming generation. ART achieves a substantial improvement over few-shot prompting and automatic CoT on unseen tasks in the BigBench and MMLU benchmarks, and matches performance of hand-crafted CoT prompts on a majority of these tasks. ART is also extensible, and makes it easy for humans to improve performance by correcting errors in task-specific programs or incorporating new tools, which we demonstrate by drastically improving performance on select tasks with minimal human intervention.

Verifying the reliability of complex, multi-step reasoning in Large Language Models (LLMs) remains a fundamental challenge, as existing methods often lack both faithfulness and precision. To address this issue, we propose the Graph of Verification (GoV) framework. GoV offers three key contributions: First, it explicitly models the underlying deductive process as a directed acyclic graph (DAG), whether this structure is implicit or explicitly constructed. Second, it enforces a topological order over the DAG to guide stepwise verification. Third, GoV introduces the notion of customizable node blocks, which flexibly define the verification granularity, from atomic propositions to full paragraphs, while ensuring that all requisite premises derived from the graph are provided as contextual input for each verification unit. We evaluate GoV on the Number Triangle Summation task and the ProcessBench benchmark with varying levels of reasoning complexity. Experimental results show that GoV substantially improves verification accuracy, faithfulness, and error localization when compared to conventional end-to-end verification approaches. Our code and data are available at https://github.com/Frevor/Graph-of-Verification.

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.

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

Reasoning Large Language Models (RLLMs) have recently achieved remarkable progress on complex reasoning tasks, largely enabled by their long chain-of-thought (Long CoT) capabilities. However, developing these Long CoT behaviors relies heavily on post-training with high-quality datasets, which are typically costly and human-curated (e.g., mathematics and code), leaving scalable alternatives unexplored. In this work, we introduce NP-hard (NPH) graph problems as a novel synthetic training corpus, as they inherently require deep reasoning, extensive exploration, and reflective strategies, which are core characteristics of Long CoT reasoning. Building on this insight, we develop a two-stage post-training framework: (i) Long CoT Supervised Fine-Tuning (SFT) on rejection-sampled NPH graph instances, which substantially enhances reasoning depth, and (ii) Reinforcement Learning (RL) with a fine-grained reward design, which sharpens reasoning efficiency. Our flagship model, Graph-R1-7B, demonstrates strong generalization across mathematics, coding, STEM, and logic, and surpasses QwQ-32B on NPH graph problems in both accuracy and reasoning efficiency. These results position NPH graph problems as an effective and scalable resource for advancing Long CoT reasoning in LLMs, opening a new frontier for LLM post-training. Our implementation is available at https://github.com/Graph-Reasoner/Graph-R1, with models and datasets hosted in our Hugging Face collection HKUST-DSAIL/Graph-R1.

Small language models (SLMs) are increasingly paired with knowledge graphs (KGs), yet end-to-end KG question answering conflates graph access, search, navigation, reasoning, and answer generation. This coupling makes it difficult both to determine whether an SLM can faithfully execute the reasoning path implied by a question and to attribute failures to navigation rather than to other stages of the pipeline. We isolate this capability by employing the THESEUS navigation and traceability framework and using frozen, off-the-shelf SLMs as local action policies. At each hop, the environment exposes the legal outgoing graph actions, and the model selects one executable graph action and decides whether to stop, without task-specific parameter updates, model-controlled beam search, or free-form answer generation. This controlled setting allows us to evaluate terminal-answer accuracy with Hits@1 together with path fidelity, using Path Edit Distance (PED) as the primary trajectory metric. Across the Kinship and MQuAKE-ST KGQAs, similarly sized local models differ substantially in answer accuracy and path fidelity, with the two metrics sometimes favoring different models. This model-dependent behavior also extends to prompting, as a single demonstrated trajectory can improve or degrade navigation depending on the model. These results motivate evaluating SLM graph reasoning beyond endpoint accuracy alone.

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.

Forecasting future links is a central task in temporal graph (TG) reasoning, requiring models to leverage historical interactions to predict upcoming ones. Traditional neural approaches, such as temporal graph neural networks, achieve strong performance but lack explainability and cannot be applied to unseen graphs without retraining. Recent studies have begun to explore using large language models (LLMs) for graph reasoning, but most of them are constrained to static graphs or small synthetic TGs and lack the evaluation of the quality of reasoning traces generated by LLMs. In this work, we present Reasoning-Enhanced Learning for Temporal Graphs (ReaL-TG), a reinforcement learning framework that fine-tunes LLMs to perform explainable link forecasting on real-world TGs. ReaL-TG uses outcome-based reward to encourage models to self-explore reasoning strategies from graph structure and to produce explanations that directly justify their predictions. To enable evaluation on LLM-generated reasoning traces, we propose a new evaluation protocol combining ranking metrics with an LLM-as-a-Judge system that assesses both the quality of reasoning and the impact of hallucinations. Experiments with ReaL-TG-4B, obtained by fine-tuning Qwen3-4B under our framework, show that it outperforms much larger frontier LLMs, including GPT-5 mini, on ranking metrics, while producing high-quality explanations confirmed by both the LLM judge and human evaluation.

Counterfactual reasoning requires models to reason beyond the observed world and explain how altered conditions propagate through downstream consequences. Existing benchmarks largely target bounded settings with fixed variables or single gold outcomes, overlooking open-domain scenarios requiring causal-process evaluation. To this end, we present WhatIfBench, a diagnostic benchmark for open-domain, open-form, long-horizon counterfactual causal reasoning, containing 220 what-if questions across STEM, HSS, and Hybrid scenarios. To evaluate free-form responses, we further propose PRISM, which first converts each natural-language explanation into a Response-Derived Semantic Causal Graph of events, states, and mechanisms. On top of this graph, PRISM then jointly applies a Process Metric assessing graph-level causal validity and a Rubric Metric assessing answer-level explanatory adequacy. Evaluating six frontier LLMs with this framework, we find that WhatIfBench remains far from saturated: even the strongest model reaches only a 64.62% final score. Further analysis reveals persistent causal gaps, premise drift, and topology fragmentation, suggesting that fluent counterfactual narratives often mask fragile causal processes. The benchmark, code, and evaluation scripts are available at https://github.com/zju-gt/WhatIfBench{WhatIfBench}.

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.

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.

Knowledge Graph-based Question Answering (KGQA) plays a pivotal role in complex reasoning tasks but remains constrained by two persistent challenges: the structural heterogeneity of Knowledge Graphs(KGs) often leads to semantic mismatch during retrieval, while existing reasoning path retrieval methods lack a global structural perspective. To address these issues, we propose Structure-Tracing Evidence Mining (STEM), a novel framework that reframes multi-hop reasoning as a schema-guided graph search task. First, we design a Semantic-to-Structural Projection pipeline that leverages KG structural priors to decompose queries into atomic relational assertions and construct an adaptive query schema graph. Subsequently, we execute globally-aware node anchoring and subgraph retrieval to obtain the final evidence reasoning graph from KG. To more effectively integrate global structural information during the graph construction process, we design a Triple-Dependent GNN (Triple-GNN) to generate a Global Guidance Subgraph (Guidance Graph) that guides the construction. STEM significantly improves both the accuracy and evidence completeness of multi-hop reasoning graph retrieval, and achieves State-of-the-Art performance on multiple multi-hop benchmarks.

Large Language Models (LLMs) have excelled in multi-hop question-answering (M-QA) due to their advanced reasoning abilities. However, the impact of the inherent reasoning structures on LLM M-QA performance remains unclear, largely due to the absence of QA datasets that provide fine-grained reasoning structures. To address this gap, we introduce the Graph Reasoning-Structured Question Answering Dataset (GRS-QA), which includes both semantic contexts and reasoning structures for QA pairs. Unlike existing M-QA datasets, where different reasoning structures are entangled together, GRS-QA explicitly captures intricate reasoning pathways by constructing reasoning graphs, where nodes represent textual contexts and edges denote logical flows. These reasoning graphs of different structures enable a fine-grained evaluation of LLM reasoning capabilities across various reasoning structures. Our empirical analysis reveals that LLMs perform differently when handling questions with varying reasoning structures. This finding facilitates the exploration of textual structures as compared with semantics.

Scripting interfaces enable users to automate tasks and customize software workflows, but creating scripts traditionally requires programming expertise and familiarity with specific APIs, posing barriers for many users. While Large Language Models (LLMs) can generate code from natural language queries, runtime code generation is severely limited due to unverified code, security risks, longer response times, and higher computational costs. To bridge the gap, we propose an offline simulation framework to curate a software-specific skillset, a collection of verified scripts, by exploiting LLMs and publicly available scripting guides. Our framework comprises two components: (1) task creation, using top-down functionality guidance and bottom-up API synergy exploration to generate helpful tasks; and (2) skill generation with trials, refining and validating scripts based on execution feedback. To efficiently navigate the extensive API landscape, we introduce a Graph Neural Network (GNN)-based link prediction model to capture API synergy, enabling the generation of skills involving underutilized APIs and expanding the skillset's diversity. Experiments with Adobe Illustrator demonstrate that our framework significantly improves automation success rates, reduces response time, and saves runtime token costs compared to traditional runtime code generation. This is the first attempt to use software scripting interfaces as a testbed for LLM-based systems, highlighting the advantages of leveraging execution feedback in a controlled environment and offering valuable insights into aligning AI capabilities with user needs in specialized software domains.

Chain-of-thought (CoT) traces have been shown to improve performance of large language models on a plethora of reasoning tasks, yet there is no consensus on the mechanism by which this boost is achieved. To shed more light on this, we introduce Causal CoT Graphs (CCGraphs), which are directed acyclic graphs automatically extracted from reasoning traces that model fine-grained causal dependencies in language-model outputs. A collection of 1671 mathematical reasoning problems from MATH500, GSM8K, and AIME, together with their associated CCGraphs, has been compiled into our dataset -- KisMATH. Our detailed empirical analysis with 15 open-weight LLMs shows that (i) reasoning nodes in the CCGraphs are causal contributors to the final answer, which we argue is constitutive of reasoning; and (ii) LLMs emphasize the reasoning paths captured by the CCGraphs, indicating that the models internally realize structures similar to our graphs. KisMATH enables controlled, graph-aligned interventions and opens avenues for further investigation into the role of CoT in LLM reasoning.

Since the introduction of the Model Context Protocol (MCP), the number of available tools for Large Language Models (LLMs) has increased significantly. These task-specific tool sets offer an alternative to general-purpose tools such as web browsers, while being easier to develop and maintain than GUIs. However, current general-purpose agents predominantly rely on web browsers for interacting with the environment. Here, we introduce TheMCPCompany, a benchmark for evaluating tool-calling agents on tasks that involve interacting with various real-world services. We use the REST APIs of these services to create MCP servers, which include over 18,000 tools. We also provide manually annotated ground-truth tools for each task. In our experiments, we use the ground truth tools to show the potential of tool-calling agents for both improving performance and reducing costs assuming perfect tool retrieval. Next, we explore agent performance using tool retrieval to study the real-world practicality of tool-based agents. While all models with tool retrieval perform similarly or better than browser-based agents, smaller models cannot take full advantage of the available tools through retrieval. On the other hand, GPT-5's performance with tool retrieval is very close to its performance with ground-truth tools. Overall, our work shows that the most advanced reasoning models are effective at discovering tools in simpler environments, but seriously struggle with navigating complex enterprise environments. TheMCPCompany reveals that navigating tens of thousands of tools and combining them in non-trivial ways to solve complex problems is still a challenging task for current models and requires both better reasoning and better retrieval models.

Reasoning-acting frameworks enhance large language models (LLMs) by interleaving reasoning with actions for dynamic information acquisition. However, extending this paradigm to graph learning remains underexplored. Graph data is inherently structured, with information distributed across nodes and edges and encoded through both topology and latent representations. As a result, effective reasoning over graphs requires not only retrieving informative evidence from the graph, but also progressively refining the accumulated context during multi-step inference. In this work, we propose GraphReAct, a graph reasoning-acting framework that enables step-by-step inference over graph-structured data. Specifically, we design a graph-based action space with two complementary retrieval actions: topological retrieval, which captures local structural dependencies, and semantic retrieval, which accesses non-local but relevant evidence in the representation space. These actions dynamically expand the reasoning context. To further support multi-step reasoning, we introduce another type of action, context refinement, which distills and reorganizes accumulated information into a compact representation. By interleaving reasoning with both retrieval and refinement actions, our framework enables a progressive transition from context expansion to compression. Extensive experiments on six benchmark datasets demonstrate that GraphReAct consistently outperforms state-of-the-art methods, validating the effectiveness of reasoning-acting for graph learning.

Knowledge graph question answering (KGQA) presents significant challenges due to the structural and semantic variations across input graphs. Existing works rely on Large Language Model (LLM) agents for graph traversal and retrieval; an approach that is sensitive to traversal initialization, as it is prone to entity linking errors and may not generalize well to custom ("bring-your-own") KGs. We introduce BYOKG-RAG, a framework that enhances KGQA by synergistically combining LLMs with specialized graph retrieval tools. In BYOKG-RAG, LLMs generate critical graph artifacts (question entities, candidate answers, reasoning paths, and OpenCypher queries), and graph tools link these artifacts to the KG and retrieve relevant graph context. The retrieved context enables the LLM to iteratively refine its graph linking and retrieval, before final answer generation. By retrieving context from different graph tools, BYOKG-RAG offers a more general and robust solution for QA over custom KGs. Through experiments on five benchmarks spanning diverse KG types, we demonstrate that BYOKG-RAG outperforms the second-best graph retrieval method by 4.5% points while showing better generalization to custom KGs. BYOKG-RAG framework is open-sourced at https://github.com/awslabs/graphrag-toolkit.

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.

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.

Understanding how events in a scenario causally connect with each other is important for effectively modeling and reasoning about events. But event reasoning remains a difficult challenge, and despite recent advances, Large Language Models (LLMs) still struggle to accurately identify causal connections between events. This struggle leads to poor performance on deeper reasoning tasks like event forecasting and timeline understanding. To address this challenge, we investigate the generation of causal event graphs (e.g., A enables B) as a parallel mechanism to help LLMs explicitly represent causality during inference. This paper evaluates both how to generate correct graphs as well as how graphs can assist reasoning. We propose a collaborative approach to causal graph generation where we use LLMs to simulate experts that focus on specific semantic relations. The experts engage in multiple rounds of discussions which are then consolidated by a final expert. Then, to demonstrate the utility of causal graphs, we use them on multiple downstream applications, and also introduce a new explainable event prediction task that requires a causal chain of events in the explanation. These explanations are more informative and coherent than baseline generations. Finally, our overall approach not finetuned on any downstream task, achieves competitive results with state-of-the-art models on both forecasting and next event prediction tasks.

LLM-based agents have demonstrated strong capabilities in data-intensive analytical tasks, yet their outputs are rarely verifiable: a reliance on linear text trajectories makes their reasoning difficult to audit. In particular, deterministic computations over raw data and semantic deductions over natural-language claims are often entangled in an unstructured stream, leaving numerical conclusions hard to reproduce and qualitative judgments hard to inspect. To address this, we propose VeriGraph, a traceable neuro-symbolic reasoning framework that enables agents to construct an explicit heterogeneous evidence directed acyclic graph (DAG) during execution. VeriGraph introduces three evidence-expansion primitives, namely computational, grounding, and derivational expansion, to connect raw data, interpreter variables, computed results, and natural-language claims in a unified graph. Under this formulation, structural traceability is reduced to graph reachability from raw data sources to terminal claims, while semantic support is measured by claim-level evidence evaluation. To improve graph construction, we further design a graph-based policy optimization strategy with a composite reward that jointly supervises answer correctness, computational integrity, and derivational coherence. Experiments on four benchmarks show that VeriGraph-8B achieves the highest overall score among all baselines. More importantly, VeriGraph produces auditable evidence graphs with substantially stronger claim grounding, achieving a 87.61\% Grounding Rate under our claim-level evidence support evaluation. These results suggest that explicit evidence-graph construction is a promising path toward verifiable data-analytic agents. Our code is available at https://github.com/ignorejjj/VeriGraph.

Evaluating the performance of visual language models (VLMs) in graphic reasoning tasks has become an important research topic. However, VLMs still show obvious deficiencies in simulating human-level graphic reasoning capabilities, especially in complex graphic reasoning and abstract problem solving, which are less studied and existing studies only focus on simple graphics. To evaluate the performance of VLMs in complex graphic reasoning, we propose ReasonBench, the first evaluation benchmark focused on structured graphic reasoning tasks, which includes 1,613 questions from real-world intelligence tests. ReasonBench covers reasoning dimensions related to location, attribute, quantity, and multi-element tasks, providing a comprehensive evaluation of the performance of VLMs in spatial, relational, and abstract reasoning capabilities. We benchmark 11 mainstream VLMs (including closed-source and open-source models) and reveal significant limitations of current models. Based on these findings, we propose a dual optimization strategy: Diagrammatic Reasoning Chain (DiaCoT) enhances the interpretability of reasoning by decomposing layers, and ReasonTune enhances the task adaptability of model reasoning through training, all of which improves VLM performance by 33.5\%. All experimental data and code are in the repository: https://huggingface.co/datasets/cistine/ReasonBench.

Vision-language models solve geometry problems with rising accuracy, yet their intermediate states remain latent and unverifiable: a relation expressed in textual reasoning or drawing code carries no guarantee that a constraint-satisfying configuration realizes it. We observe that existing externalization methods based on rendered pixels or one-shot scripts fail to provide exact, per-action geometric guarantees. Enforcing geometric relations by algebraic definition closes this gap: the workspace becomes a constraint-checked evolving canvas. We present Draw2Think, a framework that recasts geometric reasoning from latent spatial inference into agentic interaction with the GeoGebra constraint engine. In a Propose-Draw-Verify loop, Draw2Think externalizes hypotheses onto an executable canvas, measures exact geometric quantities, and feeds structured observations back to the model, so subsequent reasoning proceeds from checked canvas state grounded by the shared workspace. This externalization makes two properties separately auditable: model-level Construction Fidelity (whether the canvas realizes the intended configuration) and engine-level Measurement Faithfulness (exact values and relations from canvas constraints). Across construction, outcome, and rendering evaluations, Draw2Think builds canvases that pass 95.9% predicate-level and 84.0% strict problem-level construction checks on GeoGoal, improves outcome accuracy by up to 4.1%/16.4% on planar/solid benchmarks, and attains 68.2%/90.5% strict/relaxed rendering scores on GenExam-math. Project page is available at https://draw2think.github.io/

Real-world documents distribute evidence across text, tables, figures, and captions within complex page layouts. Answering complex questions over such documents therefore requires more than retrieving relevant passages: systems must recover the evidence topology that connects heterogeneous evidence units. Existing GraphRAG evaluations remain largely text-centered, while multimodal document RAG benchmarks assess cross-modal retrieval and generation without directly evaluating recovery of the intended evidence topology. We introduce TOPOGRAPHRAG-BENCH, a layout-grounded benchmark for multimodal evidence reasoning in GraphRAG, comprising 2,024 questions over 201 long, visually rich documents. Questions are constructed bottom-up from text, figure, and table evidence units under three controlled topologies: single-hop retrieval, bridge-chain reasoning, and multi-source synthesis. To ensure that questions preserve their intended structure, we apply counterfactual validation for shortcut resistance, modality necessity, and evidence necessity. We evaluate text-only GraphRAG, page-level visual retrieval, and multimodal GraphRAG systems using retrieval, generation, and topology-aware reasoning metrics. Multimodal GraphRAG systems achieve the strongest overall performance, but still fail when visual-textual evidence alignment or multi-unit composition is incomplete. Text-only GraphRAG struggles when key dependencies are grounded in figures or tables, while page-level visual retrieval lacks the fine-grained structure needed for topology recovery. These findings motivate GraphRAG systems that move beyond text-derived entity relation graphs to explicitly model document layouts, cross-modal evidence alignment, and the reasoning roles of evidence units. Code and data are available at https://richardlrc.github.io/TopoGraphRAG-Bench/.

Large Language Models (LLMs) can interact with the real world by connecting with versatile external APIs, resulting in better problem-solving and task automation capabilities. Previous research primarily focuses on APIs with limited arguments from a single source or overlooks the complex dependency relationship between different APIs. However, it is essential to utilize multiple APIs collaboratively from various sources (e.g., different Apps in the iPhone), especially for complex user instructions. In this paper, we introduce AppBench, the first benchmark to evaluate LLMs' ability to plan and execute multiple APIs from various sources in order to complete the user's task. Specifically, we consider two significant challenges in multiple APIs: 1) graph structures: some APIs can be executed independently while others need to be executed one by one, resulting in graph-like execution order; and 2) permission constraints: which source is authorized to execute the API call. We have experimental results on 9 distinct LLMs; e.g., GPT-4o achieves only a 2.0\% success rate at the most complex instruction, revealing that the existing state-of-the-art LLMs still cannot perform well in this situation even with the help of in-context learning and finetuning. Our code and data are publicly available at https://github.com/ruleGreen/AppBench.

This study evaluates large language models (LLMs) in generating code from algorithm descriptions from recent NLP papers. The task requires two key competencies: (1) algorithm comprehension: synthesizing information from papers and academic literature to understand implementation logic, and (2) coding expertise: identifying dependencies and correctly implementing necessary APIs. To facilitate rigorous evaluation, we introduce SciReplicate-Bench, a benchmark of 100 tasks from 36 NLP papers published in 2024, featuring detailed annotations and comprehensive test cases. Building on SciReplicate-Bench, we propose Sci-Reproducer, a multi-agent framework consisting of a Paper Agent that interprets algorithmic concepts from literature and a Code Agent that retrieves dependencies from repositories and implement solutions. To assess algorithm understanding, we introduce reasoning graph accuracy, which quantifies similarity between generated and reference reasoning graphs derived from code comments and structure. For evaluating implementation quality, we employ execution accuracy, CodeBLEU, and repository dependency/API recall metrics. In our experiments, we evaluate various powerful Non-Reasoning LLMs and Reasoning LLMs as foundational models. The best-performing LLM using Sci-Reproducer achieves only 39% execution accuracy, highlighting the benchmark's difficulty.Our analysis identifies missing or inconsistent algorithm descriptions as key barriers to successful reproduction. We will open-source our benchmark, and code at https://github.com/xyzCS/SciReplicate-Bench.

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}

Working agents need to read diverse files, coordinate tools, and produce deliverables. Training such agents requires tasks built on many real files with verifiable results, but few pipelines exist to synthesize this kind of data. Existing pipelines either generate files with models, which lack realism and diversity, or build tasks on real files without task-specific verifiers, leaving result quality unchecked. We introduce GraphForge, an evidence-graph based framework that grounds both the task and its verification in real files. Starting from occupation-grounded seeds for controlled diversity, GraphForge assembles a workspace of real files for each seed and builds an evidence graph over their relations. Since the task statement and rubrics are both derived from this graph, task requirements are backed by the workspace files and each criterion is anchored to the files needed to verify it. An initial rollout further tests executability, and a revision agent repairs the task and rubrics against the original files before trajectories are collected. Fine-tuning Qwen3.6-27B on 2,169 GraphForge trajectories brings GDPVal to 1445.7 (+65.7) under OpenHands, and Workspace-Bench-Lite and SpreadsheetBench II to 63.7 (+7.7) and 24.0 (+13.7) under Claude Code. Rejection fine-tuning on the SFT model's own rollouts, with candidates selected by the evidence-anchored rubrics, yields further improvements on all three benchmarks, suggesting that the rubrics provide a useful selection signal. The data and models are available.

Although Large Language Models (LLMs) have demonstrated remarkable progress, their proficiency in graph-related tasks remains notably limited, hindering the development of truly general-purpose models. Previous attempts, including pretraining graph foundation models or employing supervised fine-tuning, often face challenges such as the scarcity of large-scale, universally represented graph data. We introduce G1, a simple yet effective approach demonstrating that Reinforcement Learning (RL) on synthetic graph-theoretic tasks can significantly scale LLMs' graph reasoning abilities. To enable RL training, we curate Erd\~os, the largest graph reasoning dataset to date comprising 50 diverse graph-theoretic tasks of varying difficulty levels, 100k training data and 5k test data, all drived from real-world graphs. With RL on Erd\~os, G1 obtains substantial improvements in graph reasoning, where our finetuned 3B model even outperforms Qwen2.5-72B-Instruct (24x size). RL-trained models also show strong zero-shot generalization to unseen tasks, domains, and graph encoding schemes, including other graph-theoretic benchmarks as well as real-world node classification and link prediction tasks, without compromising general reasoning abilities. Our findings offer an efficient, scalable path for building strong graph reasoners by finetuning LLMs with RL on graph-theoretic tasks, which combines the strengths of pretrained LLM capabilities with abundant, automatically generated synthetic data, suggesting that LLMs possess graph understanding abilities that RL can elicit successfully.

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.

Large language models (LLMs) achieve strong results on knowledge graph question answering (KGQA), but most benchmarks assume complete knowledge graphs (KGs) where direct supporting triples exist. This reduces evaluation to shallow retrieval and overlooks the reality of incomplete KGs, where many facts are missing and answers must be inferred from existing facts. We bridge this gap by proposing a methodology for constructing benchmarks under KG incompleteness, which removes direct supporting triples while ensuring that alternative reasoning paths required to infer the answer remain. Experiments on benchmarks constructed using our methodology show that existing methods suffer consistent performance degradation under incompleteness, highlighting their limited reasoning ability. To overcome this limitation, we present the Adaptive Graph Reasoning Agent (GR-Agent). It first constructs an interactive environment from the KG, and then formalizes KGQA as agent environment interaction within this environment. GR-Agent operates over an action space comprising graph reasoning tools and maintains a memory of potential supporting reasoning evidence, including relevant relations and reasoning paths. Extensive experiments demonstrate that GR-Agent outperforms non-training baselines and performs comparably to training-based methods under both complete and incomplete settings.

Large reasoning models (LRMs) produce reasoning traces with non-linear structures, such as backtracking and self-correction, that complicate the evaluation and monitoring of the reasoning process. We introduce ReasoningFlow, a framework that captures the discourse structures of LRM reasoning traces into fine-grained directed acyclic graphs (DAGs). We develop and validate our annotation schema through careful manual annotation of 31 traces (2.1k steps), achieving high inter-annotator agreement, then scale to automatic annotation of 1,260 traces (247.7k steps) spanning three tasks (math, science, argumentation) and five models (Qwen2.5-32B-Inst, QwQ-32B, DeepSeek-V3, DeepSeek-R1, GPT-oss-120B). By analyzing ReasoningFlow graphs, we find: (1) LRMs exhibit structurally similar traces, despite being trained from different base models and potentially non-overlapping post-training data. (2) ReasoningFlow reveals diverse fine-grained reasoning behaviors (e.g., local verification, self-reflection, and assumptions) that can be used for better reasoning trace monitorability. (3) In LRMs, most of the erroneous steps are not used to derive final answers. (4) Mechanistic causal dependencies between steps do not reflect the language-level discourse structure. We release the dataset and code in: https://github.com/jinulee-v/reasoningflow.

Tools enhance the reasoning capabilities of large language models (LLMs) in complex problem-solving tasks, but not all tasks have available tools. In the absence of predefined tools, prior works have explored instructing LLMs to generate tools on their own. However, such approaches rely heavily on the models' internal knowledge and would fail in domains beyond the LLMs' knowledge scope. To address this limitation, we propose RefTool, a reference-guided framework for automatic tool creation that leverages structured external materials such as textbooks. RefTool consists of two modules: (1) tool creation, where LLMs generate executable tools from reference content, validate them using illustrative examples, and organize them hierarchically into a toolbox; and (2) tool utilization, where LLMs navigate the toolbox structure to select and apply the appropriate tools to solve problems. Experiments on causality, physics, and chemistry benchmarks demonstrate that RefTool outperforms existing tool-creation and domain-specific reasoning methods by 11.3% on average accuracy, while being cost-efficient and broadly generalizable. Analyses reveal that grounding tool creation in references produces accurate and faithful tools, and that the hierarchical structure facilitates effective tool selection. RefTool enables LLMs to overcome knowledge limitations, demonstrating the value of grounding tool creation in external references for enhanced and generalizable reasoning.

Evaluations of large language models (LLMs) primarily emphasize convergent logical reasoning, where success is defined by producing a single correct proof. However, many real-world reasoning problems admit multiple valid derivations, requiring models to explore diverse logical paths rather than committing to one route. To address this limitation, we introduce LogicGraph, the first benchmark aimed to systematically evaluate multi-path logical reasoning, constructed via a neuro-symbolic framework that leverages backward logic generation and semantic instantiation. This pipeline yields solver-verified reasoning problems formalized by high-depth multi-path reasoning and inherent logical distractions, where each instance is associated with an exhaustive set of minimal proofs. We further propose a reference-free evaluation framework to rigorously assess model performance in both convergent and divergent regimes. Experiments on state-of-the-art language models reveal a common limitation: models tend to commit early to a single route and fail to explore alternatives, and the coverage gap grows substantially with reasoning depth. LogicGraph exposes this divergence gap and provides actionable insights to motivate future improvements. Our code and data will be released at https://github.com/kkkkarry/LogicGraph.

Graph Retrieval-Augmented Generation (GraphRAG) has shown great effectiveness in enhancing the reasoning abilities of LLMs by leveraging graph structures for knowledge representation and modeling complex real-world relationships. However, existing GraphRAG methods still face significant bottlenecks when handling complex problems that require multi-hop reasoning, as their query and retrieval phases are largely based on pre-defined heuristics and do not fully utilize the reasoning potentials of LLMs. To address this problem, we propose GraphRAG-R1, an adaptive GraphRAG framework by training LLMs with process-constrained outcome-based reinforcement learning (RL) to enhance the multi-hop reasoning ability. Our method can decompose complex problems, autonomously invoke retrieval tools to acquire necessary information, and perform effective reasoning. Specifically, we utilize a modified version of Group Relative Policy Optimization (GRPO) that supports rollout-with-thinking capability. Next, we design two process-constrained reward functions. To handle the shallow retrieval problem, we design a Progressive Retrieval Attenuation (PRA) reward to encourage essential retrievals. Then, to handle the over-thinking problem, we design Cost-Aware F1 (CAF) reward to balance the model performance with computational costs. We further design a phase-dependent training strategy, containing three training stages corresponding to cold start and these two rewards. Lastly, our method adopts a hybrid graph-textual retrieval to improve the reasoning capacity. Extensive experimental results demonstrate that GraphRAG-R1 boosts LLM capabilities in solving complex reasoning problems compared to state-of-the-art GraphRAG methods on both in-domain and out-of-domain datasets. Furthermore, our framework can be flexibly integrated with various existing retrieval methods, consistently delivering performance improvements.

Mathematical knowledge is organized around statements and their dependencies, but this structure is exposed unevenly: informal papers cite mostly at the document level, while formal libraries record fine-grained dependencies over a much smaller body of mathematics. We introduce TheoremGraph, a unified statement-level dependency graph spanning both informal and formal mathematics. On the informal side, we parse 11.7M theorem-like environments from mathematics arXiv and recover 18.3M candidate directed dependencies, each labeled by the extractor that proposed it so downstream users can trade coverage for precision. On the formal side, we release LeanGraph, a Lean 4 elaborator-level extractor producing 388,105 declaration nodes and 11.3M typed edges across 25 Lean projects. We bridge the two graphs by embedding generated natural-language slogans into a shared semantic space, linking related statements across papers and across the informal/formal divide; an LLM judge affirms 47,952 such matches above a 0.8 cosine floor, with the judge-acceptance rate rising from 48% across the floor to 87% in the >=0.9 tier. On formal concept retrieval, our name-and-signature representation with graph expansion comes within 0.5pp of LeanSearch v2's reranked Recall@10 (0.775 vs. 0.780) without an LM reranker. We release the dataset, extractors, HTTP API, and MCP interface as infrastructure for mathematical search, attribution, and retrieval-augmented reasoning, available at theoremsearch.com and huggingface.co/datasets/uw-math-ai/theorem-matching.

Large Language Models (LLMs) have made remarkable progress in mathematical reasoning, but still continue to struggle with high-precision tasks like numerical computation and formal symbolic manipulation. Integrating external tools has emerged as a promising approach to bridge this gap. Despite recent advances, existing methods struggle with three key challenges: constructing tool-integrated reasoning data, performing fine-grained optimization, and enhancing inference. To overcome these limitations, we propose THOR (Tool-Integrated Hierarchical Optimization via RL). First, we introduce TIRGen, a multi-agent actor-critic-based pipeline for constructing high-quality datasets of tool-integrated reasoning paths, aligning with the policy and generalizing well across diverse models. Second, to perform fine-grained hierarchical optimization, we introduce an RL strategy that jointly optimizes for both trajectory-level problem solving and step-level code generation. This is motivated by our key insight that the success of an intermediate tool call is a strong predictor of the final answer's correctness. Finally, THOR incorporates a self-correction mechanism that leverages immediate tool feedback to dynamically revise erroneous reasoning paths during inference. Our approach demonstrates strong generalization across diverse models, performing effectively in both reasoning and non-reasoning models. It further achieves state-of-the-art performance for models of a similar scale on multiple mathematical benchmarks, while also delivering consistent improvements on code benchmarks. Our code will be publicly available at https://github.com/JingMog/THOR.

Existing Tool-Integrated Reasoning (TIR) models have effectively extended the question-answering capabilities of LLMs by incorporating external tools. However, real-world scenarios present numerous open-ended problems where fixed tools often fail to meet task requirements. Furthermore, the lack of self-optimization mechanisms means that erroneous tool outputs can mislead the LLM's responses. Additionally, the construction of existing tools entails significant manual effort, which consequently constrains their applicability. Recognizing that the reasoning traces of LLMs encapsulate implicit problem-solving capabilities, we propose UCT, a novel training-free framework that transforms agents from tool users to tool creators. This approach harvests reasoning experiences and distills them into reusable assets. This method transforms the agent from a mere tool user into a tool creator, enabling adaptive tool creation and self-updating during the inference process. We also introduce a memory consolidation mechanism to maintain the tool library, ensuring high reusability of retained experiential memory for subsequent reasoning tasks. This novel automated tool construction paradigm continuously improves tool quality during reasoning, allowing the overall agent system to progress without additional training. Extensive experiments demonstrate that our method serves as a novel paradigm for enhancing the capabilities of TIR models. In particular, the significant performance gains achieved +20.86%uparrow and +23.04%uparrow on benchmarks across multi-domain mathematical and scientific reasoning tasks validate the self-evolving capability of the agent.

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.

Graph-based Retrieval-Augmented Generation (GraphRAG) enhances the reasoning capabilities of Large Language Models (LLMs) by grounding their responses in structured knowledge graphs. Leveraging community detection and relation filtering techniques, GraphRAG systems demonstrate inherent resistance to traditional RAG attacks, such as text poisoning and prompt injection. However, in this paper, we find that the security of GraphRAG systems fundamentally relies on the topological integrity of the underlying graph, which can be undermined by implicitly corrupting the logical connections, without altering surface-level text semantics. To exploit this vulnerability, we propose LogicPoison, a novel attack framework that targets logical reasoning rather than injecting false contents. Specifically, LogicPoison employs a type-preserving entity swapping mechanism to perturb both global logic hubs for disrupting overall graph connectivity and query-specific reasoning bridges for severing essential multi-hop inference paths. This approach effectively reroutes valid reasoning into dead ends while maintaining surface-level textual plausibility. Comprehensive experiments across multiple benchmarks demonstrate that LogicPoison successfully bypasses GraphRAG's defenses, significantly degrading performance and outperforming state-of-the-art baselines in both effectiveness and stealth. Our code is available at bluehttps://github.com/Jord8061/logicPoison.

Rapidly evolving software libraries require coding language models to use unfamiliar APIs. Yet failed solutions alone tell us little about what API knowledge models need or how to provide it. We present NovelAPIBench, an automated diagnostic framework that builds benchmarks around the API knowledge gaps of a target model. It identifies novel APIs, generates executable coding tasks with separately controllable knowledge components, and classifies failures into six categories. The framework can be rerun as models and libraries evolve. We study 21 libraries across five domains and six backbone models, with our primary benchmark comprising 1,670 tasks covering 856 APIs. Our experiments show that when supplied directly, usage examples provide the strongest standalone guidance for novel API acquisition, and combining them with signature descriptions approaches full-knowledge performance. Retrieving this knowledge from a pool of APIs yields lower accuracy than supplying only the target API's knowledge, even when retrieval finds the target. Fine-tuning on other APIs improves performance on unseen APIs mainly when external knowledge is supplied, helping models both select the target API and integrate it into the surrounding code. These findings highlight complementary roles for external API knowledge and the ability to apply it. By separating knowledge content, delivery, and use, NovelAPIBench helps diagnose what limits novel API use and guides adaptation to evolving libraries. Code and data are available at https://github.com/MAPS-research/NovelAPIBench.

Chart question-answering (QA) benchmarks aim to pose questions that require visual reasoning to correctly answer, but models can often reach solutions through shortcuts or prior familiarity with a chart based on their own background knowledge. To strictly evaluate visual reasoning, we propose counterfactual charts where the chart-question task remains fixed, but underlying chart and the corresponding answer are varied. We introduce Chartographer, a framework to reverse engineer charts into executable code, validate reconstruction fidelity, generate seed-controlled counterfactual variants, and derive new answers from executable QA logic. We apply this framework to existing chart QA datasets and evaluate proprietary and open-source vision-language models (VLMs), measuring variation sensitivity and generalizability. Counterfactual charts reveal failures hidden by single-chart performance: VLMs often fail to generalize after answering the original chart correctly. We find failures are most prevalent when updated charts require novel visual reasoning pathways.

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.

Integrating external tools into Large Foundation Models (LFMs) has emerged as a promising approach to enhance their problem-solving capabilities. While existing studies have demonstrated strong performance in tool-augmented Visual Question Answering (VQA), recent benchmarks reveal significant gaps in real-world tool-use proficiency, particularly in functionally diverse multimodal settings requiring multi-step reasoning. In this work, we introduce ToolVQA, a large-scale multimodal dataset comprising 23K instances, designed to bridge this gap. Unlike previous datasets that rely on synthetic scenarios and simplified queries, ToolVQA features real-world visual contexts and challenging implicit multi-step reasoning tasks, better aligning with real user interactions. To construct this dataset, we propose ToolEngine, a novel data generation pipeline that employs Depth-First Search (DFS) with a dynamic in-context example matching mechanism to simulate human-like tool-use reasoning. ToolVQA encompasses 10 multimodal tools across 7 diverse task domains, with an average inference length of 2.78 reasoning steps per instance. The fine-tuned 7B LFMs on ToolVQA not only achieve impressive performance on our test set but also surpass the large close-sourced model GPT-3.5-turbo on various out-of-distribution (OOD) datasets, demonstrating strong generalizability to real-world tool-use scenarios.

Large language models (LLMs) are increasingly explored for graph understanding and decision-making, while System One models such as Jev select directly from supplied options. However, the capabilities of System One models on graph-related tasks remain unclear. We introduce GraphDecide, a model-independent benchmark that combines structural task profiles, matched graph-text input contrasts and heuristic-proposal controls to diagnose graph decision performance. We evaluate Jev and related choice-based models alongside language-model baselines, covering fourteen model-interface configurations. Jev's results illustrate the benchmark's central distinctions: accurate adjacency recognition does not guarantee broader structural correctness, joint graph-text input does not consistently improve prediction, and feasible construction does not establish high solution quality. Its task contracts, candidate interfaces and scoring rules support comparison across native selectors and language-model adapters. Code and aggregate results are available at https://github.com/VictorYXL/JevGraphBench.

Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers. The corresponding open-source repository is shared on GitHub https://github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.

Graph retrieval-augmented generation (GraphRAG) has emerged as a powerful paradigm for enhancing large language models (LLMs) with external knowledge. It leverages graphs to model the hierarchical structure between specific concepts, enabling more coherent and effective knowledge retrieval for accurate reasoning.Despite its conceptual promise, recent studies report that GraphRAG frequently underperforms vanilla RAG on many real-world tasks. This raises a critical question: Is GraphRAG really effective, and in which scenarios do graph structures provide measurable benefits for RAG systems? To address this, we propose GraphRAG-Bench, a comprehensive benchmark designed to evaluate GraphRAG models onboth hierarchical knowledge retrieval and deep contextual reasoning. GraphRAG-Bench features a comprehensive dataset with tasks of increasing difficulty, coveringfact retrieval, complex reasoning, contextual summarization, and creative generation, and a systematic evaluation across the entire pipeline, from graph constructionand knowledge retrieval to final generation. Leveraging this novel benchmark, we systematically investigate the conditions when GraphRAG surpasses traditional RAG and the underlying reasons for its success, offering guidelines for its practical application. All related resources and analyses are collected for the community at https://github.com/GraphRAG-Bench/GraphRAG-Benchmark.

We introduce SymbolicAI, a versatile and modular framework employing a logic-based approach to concept learning and flow management in generative processes. SymbolicAI enables the seamless integration of generative models with a diverse range of solvers by treating large language models (LLMs) as semantic parsers that execute tasks based on both natural and formal language instructions, thus bridging the gap between symbolic reasoning and generative AI. We leverage probabilistic programming principles to tackle complex tasks, and utilize differentiable and classical programming paradigms with their respective strengths. The framework introduces a set of polymorphic, compositional, and self-referential operations for data stream manipulation, aligning LLM outputs with user objectives. As a result, we can transition between the capabilities of various foundation models endowed with zero- and few-shot learning capabilities and specialized, fine-tuned models or solvers proficient in addressing specific problems. In turn, the framework facilitates the creation and evaluation of explainable computational graphs. We conclude by introducing a quality measure and its empirical score for evaluating these computational graphs, and propose a benchmark that compares various state-of-the-art LLMs across a set of complex workflows. We refer to the empirical score as the "Vector Embedding for Relational Trajectory Evaluation through Cross-similarity", or VERTEX score for short. The framework codebase and benchmark are linked below.

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.

GraphRAG enhances large language models (LLMs) to generate quality answers for user questions by retrieving related facts from external knowledge graphs. Existing GraphRAG methods adopt a fixed graph traversal strategy for fact retrieval but we observe that user questions come in different types and require different graph traversal strategies. As such, existing GraphRAG methods are limited in effectiveness (i.e., quality of the generated answers) and/or efficiency (i.e., response time or the number of used tokens). In this paper, we propose to classify the questions according to a complete four-class taxonomy and adaptively select the appropriate graph traversal strategy for each type of questions. Our system PolyG is essentially a query planner for GraphRAG and can handle diverse questions with an unified interface and execution engine. Compared with SOTA GraphRAG methods, PolyG achieves an overall win rate of 75% on generation quality and a speedup up to 4x on response time.

We propose a fully spectral, neuro\-symbolic reasoning architecture that leverages Graph Signal Processing (GSP) as the primary computational backbone for integrating symbolic logic and neural inference. Unlike conventional reasoning models that treat spectral graph methods as peripheral components, our approach formulates the entire reasoning pipeline in the graph spectral domain. Logical entities and relationships are encoded as graph signals, processed via learnable spectral filters that control multi-scale information propagation, and mapped into symbolic predicates for rule-based inference. We present a complete mathematical framework for spectral reasoning, including graph Fourier transforms, band-selective attention, and spectral rule grounding. Experiments on benchmark reasoning datasets (ProofWriter, EntailmentBank, bAbI, CLUTRR, and ARC-Challenge) demonstrate improvements in logical consistency, interpretability, and computational efficiency over state\-of\-the\-art neuro\-symbolic models. Our results suggest that GSP provides a mathematically grounded and computationally efficient substrate for robust and interpretable reasoning systems.

While Retrieval-Augmented Generation (RAG) enhances the accuracy and relevance of responses by generative language models, it falls short in graph-based contexts where both textual and topological information are important. Naive RAG approaches inherently neglect the structural intricacies of textual graphs, resulting in a critical gap in the generation process. To address this challenge, we introduce Graph Retrieval-Augmented Generation (GRAG), which significantly enhances both the retrieval and generation processes by emphasizing the importance of subgraph structures. Unlike RAG approaches that focus solely on text-based entity retrieval, GRAG maintains an acute awareness of graph topology, which is crucial for generating contextually and factually coherent responses. Our GRAG approach consists of four main stages: indexing of k-hop ego-graphs, graph retrieval, soft pruning to mitigate the impact of irrelevant entities, and generation with pruned textual subgraphs. GRAG's core workflow-retrieving textual subgraphs followed by soft pruning-efficiently identifies relevant subgraph structures while avoiding the computational infeasibility typical of exhaustive subgraph searches, which are NP-hard. Moreover, we propose a novel prompting strategy that achieves lossless conversion from textual subgraphs to hierarchical text descriptions. Extensive experiments on graph multi-hop reasoning benchmarks demonstrate that in scenarios requiring multi-hop reasoning on textual graphs, our GRAG approach significantly outperforms current state-of-the-art RAG methods while effectively mitigating hallucinations.

Multi-hop logical reasoning over knowledge graph (KG) plays a fundamental role in many artificial intelligence tasks. Recent complex query embedding (CQE) methods for reasoning focus on static KGs, while temporal knowledge graphs (TKGs) have not been fully explored. Reasoning over TKGs has two challenges: 1. The query should answer entities or timestamps; 2. The operators should consider both set logic on entity set and temporal logic on timestamp set. To bridge this gap, we define the multi-hop logical reasoning problem on TKGs. With generated three datasets, we propose the first temporal CQE named Temporal Feature-Logic Embedding framework (TFLEX) to answer the temporal complex queries. We utilize vector logic to compute the logic part of Temporal Feature-Logic embeddings, thus naturally modeling all First-Order Logic (FOL) operations on entity set. In addition, our framework extends vector logic on timestamp set to cope with three extra temporal operators (After, Before and Between). Experiments on numerous query patterns demonstrate the effectiveness of our method.

Large Language Models (LLMs) demonstrate remarkable potential in dynamic graph reasoning, but suffer from a scaling bottleneck: current models can only handle graphs with tens of nodes, constrained by exponential reasoning overhead and finite context windows. While multi-agent systems (MAS) offer collective reasoning and topology-aware orchestration, capabilities naturally suited for graph-structured tasks, their application to dynamic graphs remains unexplored. This paper presents Scaling LLM Reasoning on Dynamic Graphs via Adaptive Spatio-Temporal Multi-Agent Collaboration (AdaSTORM), a framework that reformulates large-scale dynamic graph reasoning into two stages: (i) Adaptive Partitioning, partitioning large-scale dynamic graphs into subregions that match the model's reasoning capacity while minimizing inference cost; and (ii) Collaborative Reasoning, aligning graph partition topologies with a spatio-temporal decoupled multi-agent architecture. AdaSTORM is the first multi-agent framework tailored for dynamic graph reasoning. Extensive experiments show that AdaSTORM successfully breaks through the scaling bottleneck, scaling reasoning to thousand-node graphs with over 90% accuracy across several large-scale dynamic graph settings without external tools, significantly outperforms seven competitive baselines. Furthermore, it achieves state-of-the-art accuracy on existing benchmarks and generalizes robustly to real-world datasets. The source code is available at: https://github.com/irisorchid107/AdaSTORM/.

Large Language Models (LLMs) augmented with external tools have demonstrated remarkable capabilities in complex reasoning tasks. However, existing frameworks rely heavily on natural language reasoning to determine when tools can be invoked and whether their results should be committed, lacking formal guarantees for logical safety and verifiability. We present ToolGate, a forward execution framework that provides logical safety guarantees and verifiable state evolution for LLM tool calling. ToolGate maintains an explicit symbolic state space as a typed key-value mapping representing trusted world information throughout the reasoning process. Each tool is formalized as a Hoare-style contract consisting of a precondition and a postcondition, where the precondition gates tool invocation by checking whether the current state satisfies the required conditions, and the postcondition determines whether the tool's result can be committed to update the state through runtime verification. Our approach guarantees that the symbolic state evolves only through verified tool executions, preventing invalid or hallucinated results from corrupting the world representation. Experimental validation demonstrates that ToolGate significantly improves the reliability and verifiability of tool-augmented LLM systems while maintaining competitive performance on complex multi-step reasoning tasks. This work establishes a foundation for building more trustworthy and debuggable AI systems that integrate language models with external tools.

Large language models (LLMs) have demonstrated remarkable capabilities in complex reasoning tasks when equipped with external tools. However, current frameworks predominantly rely on sequential processing, leading to inefficient execution particularly for tasks requiring extensive tool interaction. This paper introduces Flash-Searcher, a novel parallel agent reasoning framework that fundamentally reimagines the execution paradigm from sequential chains to directed acyclic graphs (DAGs). Flash-Searcher decomposes complex tasks into subtasks with explicit dependencies, enabling concurrent execution of independent reasoning paths while maintaining logical constraints. Through dynamic workflow optimization, our framework continuously refines the execution graph based on intermediate results, effectively integrating summary module. Comprehensive evaluations across multiple benchmarks demonstrate that Flash-Searcher consistently outperforms existing approaches. Specifically, it achieves 67.7% accuracy on BrowseComp and 83% on xbench-DeepSearch, while reducing agent execution steps by up to 35% compared to current frameworks. Furthermore, when distilling this parallel reasoning pipeline into single models, we observe substantial performance gains across diverse backbone architectures, underscoring the generalizability of our methodology. Our work thus represents a significant advance in agent architecture design, offering a more scalable and efficient paradigm for complex reasoning tasks.

Code evolution is inevitable in modern software development. Changes to third-party APIs frequently break existing code and complicate maintenance, posing practical challenges for developers. While large language models (LLMs) have shown promise in code generation, they struggle to reason without a structured representation of these evolving relationships, often leading them to produce outdated APIs or invalid outputs. In this work, we propose a knowledge graph-augmented framework that decomposes the migration task into two synergistic stages: evolution path retrieval and path-informed code generation. Our approach constructs static and dynamic API graphs to model intra-version structures and cross-version transitions, enabling structured reasoning over API evolution. Both modules are trained with synthetic supervision automatically derived from real-world API diffs, ensuring scalability and minimal human effort. Extensive experiments across single-package and multi-package benchmarks demonstrate that our framework significantly improves migration accuracy, controllability, and execution success over standard LLM baselines. The source code and datasets are available at: https://github.com/kangjz1203/KCoEvo.

Generalizing to unseen graph tasks without task-pecific supervision remains challenging. Graph Neural Networks (GNNs) are limited by fixed label spaces, while Large Language Models (LLMs) lack structural inductive biases. Recent advances in Large Reasoning Models (LRMs) provide a zero-shot alternative via explicit, long chain-of-thought reasoning. Inspired by this, we propose a GNN-free approach that reformulates graph tasks--node classification, link prediction, and graph classification--as textual reasoning problems solved by LRMs. We introduce the first datasets with detailed reasoning traces for these tasks and develop Graph-R1, a reinforcement learning framework that leverages task-specific rethink templates to guide reasoning over linearized graphs. Experiments demonstrate that Graph-R1 outperforms state-of-the-art baselines in zero-shot settings, producing interpretable and effective predictions. Our work highlights the promise of explicit reasoning for graph learning and provides new resources for future research.

Repository-level fault localization (FL) and automated program repair (APR) require an agent to identify the relevant code units across files, follow call and data dependencies, and generate a valid patch. Existing graph-based systems provide structural representations of repositories (files, classes, functions and their relationships) but do not model how variable values flow within procedures, leaving agents without the semantic precision needed for function- and line-level localization. We present ARISE (Agentic Repository-level Issue Solving Engine), which augments an LLM-based agent with a multi-granularity program graph that extends structural relationships down to statement-level nodes connected by intra-procedural definition-use edges. ARISE exposes this graph through a three-tier tool API, which brings data-flow slicing as a first-class, queryable agent primitive that allows the model to trace, in a single call, which statements define or consume a variable of interest. We evaluate on SWE-bench Lite (300 real GitHub issues, 11 Python repositories) using Qwen2.5-Coder-32B-Instruct as the backbone. Compared to the unmodified SWE-agent baseline, ARISE improves Function Recall@1 by 17.0 points and Line Recall@1 by 15.0 points. These localization gains translate directly into repair success, with ARISE achieving 22.0% Pass@1 (66/300), a 4.7 percentage-point improvement over SWE-agent. Controlled ablations confirm that the improvement is driven by the data-flow graph rather than the tool schema, and that large code models consume structured slice output directly without requiring a natural-language summarization layer. The graph builder and slicing API are designed as a framework-agnostic, drop-in toolset for future APR research.

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.

Flowcharts are a critical tool for visualizing decision-making processes. However, their non-linear structure and complex visual-textual relationships make it challenging to interpret them using LLMs, as vision-language models frequently hallucinate nonexistent connections and decision paths when analyzing these diagrams. This leads to compromised reliability for automated flowchart processing in critical domains such as logistics, health, and engineering. We introduce the task of Fine-grained Flowchart Attribution, which traces specific components grounding a flowchart referring LLM response. Flowchart Attribution ensures the verifiability of LLM predictions and improves explainability by linking generated responses to the flowchart's structure. We propose FlowPathAgent, a neurosymbolic agent that performs fine-grained post hoc attribution through graph-based reasoning. It first segments the flowchart, then converts it into a structured symbolic graph, and then employs an agentic approach to dynamically interact with the graph, to generate attribution paths. Additionally, we present FlowExplainBench, a novel benchmark for evaluating flowchart attributions across diverse styles, domains, and question types. Experimental results show that FlowPathAgent mitigates visual hallucinations in LLM answers over flowchart QA, outperforming strong baselines by 10-14% on our proposed FlowExplainBench dataset.

We propose T2I-ReasonBench, a benchmark evaluating reasoning capabilities of text-to-image (T2I) models. It consists of four dimensions: Idiom Interpretation, Textual Image Design, Entity-Reasoning and Scientific-Reasoning. We propose a two-stage evaluation protocol to assess the reasoning accuracy and image quality. We benchmark various T2I generation models, and provide comprehensive analysis on their performances.

Large language models (LLMs) have displayed massive improvements in reason- ing and decision-making skills and can hold natural conversations with users. Many recent works seek to augment LLM-based assistants with external tools so they can access private or up-to-date information and carry out actions on behalf of users. To better measure the performance of these assistants, this paper introduces ToolTalk, a benchmark consisting of complex user intents re- quiring multi-step tool usage specified through dialogue. ToolTalk contains 28 tools grouped into 7 plugins, and includes a complete simulated implementa- tion of each tool, allowing for fully automated evaluation of assistants that rely on execution feedback. ToolTalk also emphasizes tools that externally affect the world rather than only tools for referencing or searching information. We evaluate GPT-3.5 and GPT-4 on ToolTalk resulting in success rates of 26% and 50% respectively. Our analysis of the errors reveals three major categories and suggests some future directions for improvement. We release ToolTalk at https://github.com/microsoft/ToolTalk.

We propose a new CogQA framework for multi-hop question answering in web-scale documents. Inspired by the dual process theory in cognitive science, the framework gradually builds a cognitive graph in an iterative process by coordinating an implicit extraction module (System 1) and an explicit reasoning module (System 2). While giving accurate answers, our framework further provides explainable reasoning paths. Specifically, our implementation based on BERT and graph neural network efficiently handles millions of documents for multi-hop reasoning questions in the HotpotQA fullwiki dataset, achieving a winning joint F_1 score of 34.9 on the leaderboard, compared to 23.6 of the best competitor.

Tool-augmented large language models have advanced from single-turn question answering to deep research workflows that iteratively plan queries, invoke external tools, and synthesize information to address complex information needs. Evaluating such workflows presents a fundamental challenge: reliance on live APIs introduces non-determinism, as tool invocations may yield different results across runs due to temporal drift, rate limiting, and evolving backend states. This variance undermines reproducibility and invalidates cross-system comparisons. We present ScholarGym, a simulation environment for reproducible evaluation of deep research workflows on academic literature. The environment decouples workflow components into query planning, tool invocation, and relevance assessment, enabling fine-grained analysis of each stage under controlled conditions. Built on a static corpus of 570K papers with deterministic retrieval, ScholarGym provides 2,536 queries with expert-annotated ground truth. Experiments across diverse backbone models reveal how reasoning capabilities, planning strategies, and selection mechanisms interact over iterative refinement.

In this paper, we propose an autonomous information seeking visual question answering framework, AVIS. Our method leverages a Large Language Model (LLM) to dynamically strategize the utilization of external tools and to investigate their outputs, thereby acquiring the indispensable knowledge needed to provide answers to the posed questions. Responding to visual questions that necessitate external knowledge, such as "What event is commemorated by the building depicted in this image?", is a complex task. This task presents a combinatorial search space that demands a sequence of actions, including invoking APIs, analyzing their responses, and making informed decisions. We conduct a user study to collect a variety of instances of human decision-making when faced with this task. This data is then used to design a system comprised of three components: an LLM-powered planner that dynamically determines which tool to use next, an LLM-powered reasoner that analyzes and extracts key information from the tool outputs, and a working memory component that retains the acquired information throughout the process. The collected user behavior serves as a guide for our system in two key ways. First, we create a transition graph by analyzing the sequence of decisions made by users. This graph delineates distinct states and confines the set of actions available at each state. Second, we use examples of user decision-making to provide our LLM-powered planner and reasoner with relevant contextual instances, enhancing their capacity to make informed decisions. We show that AVIS achieves state-of-the-art results on knowledge-intensive visual question answering benchmarks such as Infoseek and OK-VQA.

There has been considerable divergence of opinion on the reasoning abilities of Large Language Models (LLMs). While the initial optimism that reasoning might emerge automatically with scale has been tempered thanks to a slew of counterexamples, a wide spread belief in their iterative self-critique capabilities persists. In this paper, we set out to systematically investigate the effectiveness of iterative prompting of LLMs in the context of Graph Coloring, a canonical NP-complete reasoning problem that is related to propositional satisfiability as well as practical problems like scheduling and allocation. We present a principled empirical study of the performance of GPT4 in solving graph coloring instances or verifying the correctness of candidate colorings. In iterative modes, we experiment with the model critiquing its own answers and an external correct reasoner verifying proposed solutions. In both cases, we analyze whether the content of the criticisms actually affects bottom line performance. The study seems to indicate that (i) LLMs are bad at solving graph coloring instances (ii) they are no better at verifying a solution--and thus are not effective in iterative modes with LLMs critiquing LLM-generated solutions (iii) the correctness and content of the criticisms--whether by LLMs or external solvers--seems largely irrelevant to the performance of iterative prompting. We show that the observed increase in effectiveness is largely due to the correct solution being fortuitously present in the top-k completions of the prompt (and being recognized as such by an external verifier). Our results thus call into question claims about the self-critiquing capabilities of state of the art LLMs.

Fact-checking plays a crucial role in combating misinformation. Existing methods using large language models (LLMs) for claim decomposition face two key limitations: (1) insufficient decomposition, introducing unnecessary complexity to the verification process, and (2) ambiguity of mentions, leading to incorrect verification results. To address these challenges, we suggest introducing a claim graph consisting of triplets to address the insufficient decomposition problem and reduce mention ambiguity through graph structure. Based on this core idea, we propose a graph-based framework, GraphFC, for fact-checking. The framework features three key components: graph construction, which builds both claim and evidence graphs; graph-guided planning, which prioritizes the triplet verification order; and graph-guided checking, which verifies the triples one by one between claim and evidence graphs. Extensive experiments show that GraphFC enables fine-grained decomposition while resolving referential ambiguities through relational constraints, achieving state-of-the-art performance across three datasets.

Despite the advancements of open-source large language models (LLMs) and their variants, e.g., LLaMA and Vicuna, they remain significantly limited in performing higher-level tasks, such as following human instructions to use external tools (APIs). This is because current instruction tuning largely focuses on basic language tasks instead of the tool-use domain. This is in contrast to state-of-the-art (SOTA) LLMs, e.g., ChatGPT, which have demonstrated excellent tool-use capabilities but are unfortunately closed source. To facilitate tool-use capabilities within open-source LLMs, we introduce ToolLLM, a general tool-use framework of data construction, model training and evaluation. We first present ToolBench, an instruction-tuning dataset for tool use, which is created automatically using ChatGPT. Specifically, we collect 16,464 real-world RESTful APIs spanning 49 categories from RapidAPI Hub, then prompt ChatGPT to generate diverse human instructions involving these APIs, covering both single-tool and multi-tool scenarios. Finally, we use ChatGPT to search for a valid solution path (chain of API calls) for each instruction. To make the searching process more efficient, we develop a novel depth-first search-based decision tree (DFSDT), enabling LLMs to evaluate multiple reasoning traces and expand the search space. We show that DFSDT significantly enhances the planning and reasoning capabilities of LLMs. For efficient tool-use assessment, we develop an automatic evaluator: ToolEval. We fine-tune LLaMA on ToolBench and obtain ToolLLaMA. Our ToolEval reveals that ToolLLaMA demonstrates a remarkable ability to execute complex instructions and generalize to unseen APIs, and exhibits comparable performance to ChatGPT. To make the pipeline more practical, we devise a neural API retriever to recommend appropriate APIs for each instruction, negating the need for manual API selection.

Large reasoning models (LRMs) are often evaluated using metrics such as final-answer accuracy or token count. However, identical scores on these metrics can hide fundamentally different reasoning structures. To address this limitation, we introduce a scalable LRM benchmark of logic puzzles and a pipeline that converts unstructured traces into verifiable reasoning graphs of claims and dependencies. This turns reasoning into a structured, measurable object whose topology can be quantitatively analyzed. Building on this, we define a reasoning efficiency metric that quantifies how concentrated the model's logical flow is. Our analysis on open-source reasoning models shows that structural measurements separate behaviors that token count and accuracy conflate, providing a practical tool for diagnosing failure modes and comparing how reasoning scales with puzzle difficulty.

Reasoning over knowledge graphs (KGs) is a challenging task that requires a deep understanding of the complex relationships between entities and the underlying logic of their relations. Current approaches rely on learning geometries to embed entities in vector space for logical query operations, but they suffer from subpar performance on complex queries and dataset-specific representations. In this paper, we propose a novel decoupled approach, Language-guided Abstract Reasoning over Knowledge graphs (LARK), that formulates complex KG reasoning as a combination of contextual KG search and logical query reasoning, to leverage the strengths of graph extraction algorithms and large language models (LLM), respectively. Our experiments demonstrate that the proposed approach outperforms state-of-the-art KG reasoning methods on standard benchmark datasets across several logical query constructs, with significant performance gain for queries of higher complexity. Furthermore, we show that the performance of our approach improves proportionally to the increase in size of the underlying LLM, enabling the integration of the latest advancements in LLMs for logical reasoning over KGs. Our work presents a new direction for addressing the challenges of complex KG reasoning and paves the way for future research in this area.

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.

Vulnerability detection is crucial for ensuring the security and reliability of software systems. Recently, Graph Neural Networks (GNNs) have emerged as a prominent code embedding approach for vulnerability detection, owing to their ability to capture the underlying semantic structure of source code. However, GNNs face significant challenges in explainability due to their inherently black-box nature. To this end, several factual reasoning-based explainers have been proposed. These explainers provide explanations for the predictions made by GNNs by analyzing the key features that contribute to the outcomes. We argue that these factual reasoning-based explanations cannot answer critical what-if questions: What would happen to the GNN's decision if we were to alter the code graph into alternative structures? Inspired by advancements of counterfactual reasoning in artificial intelligence, we propose CFExplainer, a novel counterfactual explainer for GNN-based vulnerability detection. Unlike factual reasoning-based explainers, CFExplainer seeks the minimal perturbation to the input code graph that leads to a change in the prediction, thereby addressing the what-if questions for vulnerability detection. We term this perturbation a counterfactual explanation, which can pinpoint the root causes of the detected vulnerability and furnish valuable insights for developers to undertake appropriate actions for fixing the vulnerability. Extensive experiments on four GNN-based vulnerability detection models demonstrate the effectiveness of CFExplainer over existing state-of-the-art factual reasoning-based explainers.

We present the first systematic approach to static and dynamic taint analysis for Graph APIs focusing on broken access control. The approach comprises the following. We taint nodes in the Graph API if they represent data requiring specific privileges in order to be retrieved or manipulated, and identify API calls which are related to sources and sinks. Then, we statically analyze whether tainted information flow between API source and sink calls occurs. To this end, we model the API calls using graph transformation rules. We subsequently use critical pair analysis to automatically analyze potential dependencies between rules representing source calls and rules representing sink calls. We distinguish direct from indirect tainted information flow and argue under which conditions the CPA is able to detect not only direct, but also indirect tainted flow. The static taint analysis (i) identifies flows that need to be further reviewed, since tainted nodes may be created by an API call and used or manipulated by another API call later without having the necessary privileges, and (ii) can be used to systematically design dynamic security tests for broken access control. The dynamic taint analysis checks if potential broken access control risks detected during the static taint analysis really occur. We apply the approach to a part of the GitHub GraphQL API. The application illustrates that our analysis supports the detection of two types of broken access control systematically: the case where users of the API may not be able to access or manipulate information, although they should be able to do so; and the case where users (or attackers) of the API may be able to access/manipulate information that they should not.

Retrieval-Augmented Generation (RAG) has become a powerful and widely used approach for improving large language models by grounding generation in retrieved evidence. However, RAG systems still produce incorrect answers in many cases. Why RAG fails despite having access to external information remains poorly understood. We present a model-internal study of retrieval-augmented generation that examines how retrieved evidence influences answer generation. Using circuit tracing, we construct attribution graphs that model the flow of information through transformer layers during decoding. These graphs represent interactions among retrieved context, intermediate model activations, and generated tokens, providing a graph, circuit-level view of how external evidence is integrated into the model's reasoning process across multiple question answering benchmarks, we observe consistent structural differences: correct predictions exhibit deeper reasoning paths, more distributed evidence flow, and a more structured pattern of local connectivity, while failed predictions show shallower, fragmented, and overly concentrated evidence flow. Building on these findings, we develop a graph-based error detection framework that uses attribution-graph topology features. Furthermore, we show that attribution graphs enable targeted interventions. By reinforcing question-constrained evidence grounding, we reshape internal routing so that answer generation remains guided by the question, leading to more effective integration of retrieved information and fewer errors.

Graph Retrieval-Augmented Generation (GraphRAG) has emerged as a promising paradigm that organizes external knowledge into structured graphs of entities and relations, enabling large language models (LLMs) to perform complex reasoning beyond text-chunk retrieval. Recent advances have integrated reinforcement learning (RL) into agentic GraphRAG approaches, enabling iterative interactions with knowledge graphs during training. However, existing RL-based methods suffer from two key limitations: (1) they primarily depend on semantic similarity for retrieval, often overlooking the underlying graph topology, and (2) they rely on sparse, outcome-level rewards that fail to capture the quality of intermediate retrieval steps and their dependencies. To address these limitations, we propose HyperGraphPro, a progress-aware agentic framework for graph-based retrieval and multi-step reasoning. HyperGraphPro introduces a structure-aware hypergraph retrieval mechanism that jointly considers semantic relevance and graph connectivity, promoting coherent traversal along multi-hop reasoning paths. Furthermore, we design a progress-based stepwise policy optimization that provides dense learning signals by modulating advantages according to intermediate reasoning progress within a graph, rather than relying solely on final outcomes. Experiments on multi-hop question answering benchmarks demonstrate that HyperGraphPro consistently improves reasoning accuracy and generation quality over existing GraphRAG methods.

Large Language Models (LLMs) have shown strong inductive reasoning ability across various domains, but their reliability is hindered by the outdated knowledge and hallucinations. Retrieval-Augmented Generation mitigates these issues by grounding LLMs with external knowledge; however, most existing RAG pipelines rely on unstructured text, limiting interpretability and structured reasoning. Knowledge graphs, which represent facts as relational triples, offer a more structured and compact alternative. Recent studies have explored integrating knowledge graphs with LLMs for knowledge graph question answering (KGQA), with a significant proportion adopting the retrieve-then-reasoning paradigm. In this framework, graph-based retrievers have demonstrated strong empirical performance, yet they still face challenges in generalization ability. In this work, we propose RAPL, a novel framework for efficient and effective graph retrieval in KGQA. RAPL addresses these limitations through three aspects: (1) a two-stage labeling strategy that combines heuristic signals with parametric models to provide causally grounded supervision; (2) a model-agnostic graph transformation approach to capture both intra- and inter-triple interactions, thereby enhancing representational capacity; and (3) a path-based reasoning strategy that facilitates learning from the injected rational knowledge, and supports downstream reasoner through structured inputs. Empirically, RAPL outperforms state-of-the-art methods by 2.66%-20.34%, and significantly reduces the performance gap between smaller and more powerful LLM-based reasoners, as well as the gap under cross-dataset settings, highlighting its superior retrieval capability and generalizability. Codes are available at: https://github.com/tianyao-aka/RAPL.

Extensive research has investigated the integration of large language models (LLMs) with knowledge graphs to enhance the reasoning process. However, understanding how models perform reasoning utilizing structured graph knowledge remains underexplored. Most existing approaches rely on LLMs or retrievers to make binary judgments regarding the utilization of knowledge, which is too coarse. Meanwhile, there is still a lack of feedback mechanisms for reflection and correction throughout the entire reasoning path. This paper proposes an Active self-Reflection framework for knowledge Graph reasoning ARG, introducing for the first time an end-to-end training approach to achieve iterative reasoning grounded on structured graphs. Within the framework, the model leverages special tokens to actively determine whether knowledge retrieval is necessary, performs reflective critique based on the retrieved knowledge, and iteratively reasons over the knowledge graph. The reasoning paths generated by the model exhibit high interpretability, enabling deeper exploration of the model's understanding of structured knowledge. Ultimately, the proposed model achieves outstanding results compared to existing baselines in knowledge graph reasoning tasks.

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 recently been extended beyond traditional text generation to serve as interactive agents capable of using external tools based on user intent. However, current LLM agents still show limited ability to handle goal-oriented queries, which require decomposing a high-level objective into multiple interdependent API calls with correct planning and execution. Current approaches mainly rely on zero-shot evaluation due to the absence of training data. While proprietary closed-source models such as GPT-4 demonstrate strong reasoning abilities, smaller open-source models struggle to perform complex tool use effectively. Thus, we propose a novel training framework GOAT, which enables fine-tuning of LLM agents in a human annotation-free setting. GOAT automatically constructs synthetic datasets of goal-oriented API execution tasks directly from given API documents, equipping models with the ability to reason over interdependent calls and generate coherent responses. Through extensive experiments, we show that GOAT-trained agents achieve state-of-the-art performance across multiple existing goal-oriented benchmarks. In addition, we introduce GOATBench, a new goal-oriented API execution benchmark, and demonstrate that agents trained with GOAT also excel in this setting. These results highlight GOAT as a practical path toward building robust open-source LLM agents capable of complex reasoning and tool use.

Large Language Models (LLMs) have demonstrated impressive performance in various NLP tasks, but they still suffer from challenges such as hallucination and weak numerical reasoning. To overcome these challenges, external tools can be used to enhance LLMs' question-answering abilities. However, current evaluation methods do not distinguish between questions that can be answered using LLMs' internal knowledge and those that require external information through tool use. To address this issue, we introduce a new dataset called ToolQA, which is designed to faithfully evaluate LLMs' ability to use external tools for question answering. Our development of ToolQA involved a scalable, automated process for dataset curation, along with 13 specialized tools designed for interaction with external knowledge in order to answer questions. Importantly, we strive to minimize the overlap between our benchmark data and LLMs' pre-training data, enabling a more precise evaluation of LLMs' tool-use reasoning abilities. We conducted an in-depth diagnosis of existing tool-use LLMs to highlight their strengths, weaknesses, and potential improvements. Our findings set a new benchmark for evaluating LLMs and suggest new directions for future advancements. Our data and code are freely available to the broader scientific community on GitHub.

Language model (LM) agents, such as SWE-agent and OpenHands, have made progress toward automated issue resolution. However, existing approaches are often limited to Python-only issues and rely on pre-constructed containers in SWE-bench with reproduced issues, restricting their applicability to real-world and work for multi-language repositories. We present Prometheus, designed to resolve real-world issues beyond benchmark settings. Prometheus is a multi-agent system that transforms an entire code repository into a unified knowledge graph to guide context retrieval for issue resolution. Prometheus encodes files, abstract syntax trees, and natural language text into a graph of typed nodes and five general edge types to support multiple programming languages. Prometheus uses Neo4j for graph persistence, enabling scalable and structured reasoning over large codebases. Integrated by the DeepSeek-V3 model, Prometheus resolves 28.67% and 13.7% of issues on SWE-bench Lite and SWE-bench Multilingual, respectively, with an average API cost of 0.23 and 0.38 per issue. Prometheus resolves 10 unique issues not addressed by prior work and is the first to demonstrate effectiveness across seven programming languages. Moreover, it shows the ability to resolve real-world GitHub issues in the LangChain and OpenHands repositories. We have open-sourced Prometheus at: https://github.com/Pantheon-temple/Prometheus

Augmented Language Models (ALMs) blend the reasoning capabilities of Large Language Models (LLMs) with tools that allow for knowledge retrieval and action execution. Existing ALM systems trigger LLM thought processes while pulling observations from these tools in an interleaved fashion. Specifically, an LLM reasons to call an external tool, gets halted to fetch the tool's response, and then decides the next action based on all preceding response tokens. Such a paradigm, though straightforward and easy to implement, often leads to huge computation complexity from redundant prompts and repeated execution. This study addresses such challenges for the first time, proposing a modular paradigm ReWOO (Reasoning WithOut Observation) that detaches the reasoning process from external observations, thus significantly reducing token consumption. Comprehensive evaluations across six public NLP benchmarks and a curated dataset reveal consistent performance enhancements with our proposed methodology. Notably, ReWOO achieves 5x token efficiency and 4% accuracy improvement on HotpotQA, a multi-step reasoning benchmark. Furthermore, ReWOO demonstrates robustness under tool-failure scenarios. Beyond prompt efficiency, decoupling parametric modules from non-parametric tool calls enables instruction fine-tuning to offload LLMs into smaller language models, thus substantially reducing model parameters. Our illustrative work offloads reasoning ability from 175B GPT3.5 into 7B LLaMA, demonstrating the significant potential for truly efficient and scalable ALM systems.

Graph Retrieval-Augmented Generation (Graph-RAG) enhances multihop question answering by organizing corpora into knowledge graphs and routing evidence through relational structure. However, practical deployments face two persistent bottlenecks: (i) mixed-difficulty workloads where one-size-fits-all retrieval either wastes cost on easy queries or fails on hard multihop cases, and (ii) extraction loss, where graph abstraction omits fine-grained qualifiers that remain only in source text. We present A2RAG, an adaptive-and-agentic GraphRAG framework for cost-aware and reliable reasoning. A2RAG couples an adaptive controller that verifies evidence sufficiency and triggers targeted refinement only when necessary, with an agentic retriever that progressively escalates retrieval effort and maps graph signals back to provenance text to remain robust under extraction loss and incomplete graphs. Experiments on HotpotQA and 2WikiMultiHopQA demonstrate that A2RAG achieves +9.9/+11.8 absolute gains in Recall@2, while cutting token consumption and end-to-end latency by about 50% relative to iterative multihop baselines.

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.

Large Language Models (LLMs) exhibit strong reasoning capabilities in complex tasks. However, they still struggle with hallucinations and factual errors in knowledge-intensive scenarios like knowledge graph question answering (KGQA). We attribute this to the semantic gap between structured knowledge graphs (KGs) and unstructured queries, caused by inherent differences in their focuses and structures. Existing methods usually employ resource-intensive, non-scalable workflows reasoning on vanilla KGs, but overlook this gap. To address this challenge, we propose a flexible framework, Enrich-on-Graph (EoG), which leverages LLMs' prior knowledge to enrich KGs, bridge the semantic gap between graphs and queries. EoG enables efficient evidence extraction from KGs for precise and robust reasoning, while ensuring low computational costs, scalability, and adaptability across different methods. Furthermore, we propose three graph quality evaluation metrics to analyze query-graph alignment in KGQA task, supported by theoretical validation of our optimization objectives. Extensive experiments on two KGQA benchmark datasets indicate that EoG can effectively generate high-quality KGs and achieve the state-of-the-art performance. Our code and data are available at https://github.com/zjukg/Enrich-on-Graph.

External tools help large language models succeed at tasks where they would otherwise typically fail. In existing frameworks, choosing tools at test time relies on naive greedy decoding, regardless of whether the model has been fine-tuned on tool-annotated data or prompted with in-context examples. In contrast, we find that gathering and choosing among a suitable set of candidate tools has greater potential to lead to an optimal selection. We present Tool selECTion via meta-reasONing (TECTON), a two-phase system that first reasons over a task and outputs candidate tools using a custom fine-tuned language modelling head. Then, with the custom head disabled, it meta-reasons (i.e., it reasons over the previous reasoning process) to make a final choice. We show that TECTON results in substantial gains--both in-distribution and out-of-distribution--on a range of math reasoning datasets.