Graph-based Agent Memory: Taxonomy, Techniques, and Applications

Memory emerges as the core module in the Large Language Model (LLM)-based agents for long-horizon complex tasks (e.g., multi-turn dialogue, game playing, scientific discovery), where memory can enable knowledge accumulation, iterative reasoning and self-evolution. Among diverse paradigms, graph stands out as a powerful structure for agent memory due to the intrinsic capabilities to model relational dependencies, organize hierarchical information, and support efficient retrieval. This survey presents a comprehensive review of agent memory from the graph-based perspective. First, we introduce a taxonomy of agent memory, including short-term vs. long-term memory, knowledge vs. experience memory, non-structural vs. structural memory, with an implementation view of graph-based memory. Second, according to the life cycle of agent memory, we systematically analyze the key techniques in graph-based agent memory, covering memory extraction for transforming the data into the contents, storage for organizing the data efficiently, retrieval for retrieving the relevant contents from memory to support reasoning, and evolution for updating the contents in the memory. Third, we summarize the open-sourced libraries and benchmarks that support the development and evaluation of self-evolving agent memory. We also explore diverse application scenarios. Finally, we identify critical challenges and future research directions. This survey aims to offer actionable insights to advance the development of more efficient and reliable graph-based agent memory systems. All the related resources, including research papers, open-source data, and projects, are collected for the community in https://github.com/DEEP-PolyU/Awesome-GraphMemory.

Use Graph When It Needs: Efficiently and Adaptively Integrating Retrieval-Augmented Generation with Graphs

Large language models (LLMs) often struggle with knowledge-intensive tasks due to hallucinations and outdated parametric knowledge. While Retrieval-Augmented Generation (RAG) addresses this by integrating external corpora, its effectiveness is limited by fragmented information in unstructured domain documents. Graph-augmented RAG (GraphRAG) emerged to enhance contextual reasoning through structured knowledge graphs, yet paradoxically underperforms vanilla RAG in real-world scenarios, exhibiting significant accuracy drops and prohibitive latency despite gains on complex queries. We identify the rigid application of GraphRAG to all queries, regardless of complexity, as the root cause. To resolve this, we propose an efficient and adaptive GraphRAG framework called EA-GraphRAG that dynamically integrates RAG and GraphRAG paradigms through syntax-aware complexity analysis. Our approach introduces: (i) a syntactic feature constructor that parses each query and extracts a set of structural features; (ii) a lightweight complexity scorer that maps these features to a continuous complexity score; and (iii) a score-driven routing policy that selects dense RAG for low-score queries, invokes graph-based retrieval for high-score queries, and applies complexity-aware reciprocal rank fusion to handle borderline cases. Extensive experiments on a comprehensive benchmark, consisting of two single-hop and two multi-hop QA benchmarks, demonstrate that our EA-GraphRAG significantly improves accuracy, reduces latency, and achieves state-of-the-art performance in handling mixed scenarios involving both simple and complex queries.

BAPO: Boundary-Aware Policy Optimization for Reliable Agentic Search

RL-based agentic search enables LLMs to solve complex questions via dynamic planning and external search. While this approach significantly enhances accuracy with agent policies optimized via large-scale reinforcement learning, we identify a critical gap in reliability: these agents fail to recognize their reasoning boundaries and rarely admit ``I DON'T KNOW'' (IDK) even when evidence is insufficient or reasoning reaches its limit. The lack of reliability often leads to plausible but unreliable answers, introducing significant risks in many real-world scenarios. To this end, we propose Boundary-Aware Policy Optimization (BAPO), a novel RL framework designed to cultivate reliable boundary awareness without compromising accuracy. BAPO introduces two key components: (i) a group-based boundary-aware reward that encourages an IDK response only when the reasoning reaches its limit, and (ii) an adaptive reward modulator that strategically suspends this reward during early exploration, preventing the model from exploiting IDK as a shortcut. Extensive experiments on four benchmarks demonstrate that BAPO substantially enhances the overall reliability of agentic search.

Probing Latent Knowledge Conflict for Faithful Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) has emerged as a powerful paradigm to enhance the factuality of Large Language Models (LLMs). However, existing RAG systems often suffer from an unfaithfulness issue, where the model's response contradicts evidence from the retrieved context. Existing approaches to improving contextual faithfulness largely rely on external interventions, such as prompt engineering, decoding constraints, or reward-based fine-tuning. These works treat the LLM as a black box and overlook a crucial question: how does the LLM internally integrate retrieved evidence with its parametric memory, particularly under knowledge conflicts? To address this gap, we conduct a probing-based analysis of hidden-state representations in LLMs and observe three findings: knowledge integration occurs hierarchically, conflicts manifest as latent signals at the sentence level, and irrelevant context is often amplified when aligned with parametric knowledge. Building on these findings, we propose CLEAR (Conflict-Localized and Enhanced Attention for RAG), a framework that (i) decomposes context into fine-grained sentence-level knowledge, (ii) employs hidden-state probing to localize conflicting knowledge, and (iii) introduces conflict-aware fine-tuning to guide the model to accurately integrate retrieved evidence. Extensive experiments across three benchmarks demonstrate that CLEAR substantially improves both accuracy and contextual faithfulness, consistently outperforming strong baselines under diverse conflict conditions. The related resources are available at https://github.com/LinfengGao/CLEAR.

LoSemB: Logic-Guided Semantic Bridging for Inductive Tool Retrieval

Tool learning has emerged as a promising paradigm for large language models (LLMs) to solve many real-world tasks. Nonetheless, with the tool repository rapidly expanding, it is impractical to contain all tools within the limited input length of LLMs. To alleviate these issues, researchers have explored incorporating a tool retrieval module to select the most relevant tools or represent tools as unique tokens within LLM parameters. However, most state-of-the-art methods are under transductive settings, assuming all tools have been observed during training. Such a setting deviates from reality as the real-world tool repository is evolving and incorporates new tools frequently. When dealing with these unseen tools, which refer to tools not encountered during the training phase, these methods are limited by two key issues, including the large distribution shift and the vulnerability of similarity-based retrieval. To this end, inspired by human cognitive processes of mastering unseen tools through discovering and applying the logical information from prior experience, we introduce a novel Logic-Guided Semantic Bridging framework for inductive tool retrieval, namely, LoSemB, which aims to mine and transfer latent logical information for inductive tool retrieval without costly retraining. Specifically, LoSemB contains a logic-based embedding alignment module to mitigate distribution shifts and implements a relational augmented retrieval mechanism to reduce the vulnerability of similarity-based retrieval. Extensive experiments demonstrate that LoSemB achieves advanced performance in inductive settings while maintaining desirable effectiveness in the transductive setting.

Mol-R1: Towards Explicit Long-CoT Reasoning in Molecule Discovery

Large language models (LLMs), especially Explicit Long Chain-of-Thought (CoT) reasoning models like DeepSeek-R1 and QWQ, have demonstrated powerful reasoning capabilities, achieving impressive performance in commonsense reasoning and mathematical inference. Despite their effectiveness, Long-CoT reasoning models are often criticized for their limited ability and low efficiency in knowledge-intensive domains such as molecule discovery. Success in this field requires a precise understanding of domain knowledge, including molecular structures and chemical principles, which is challenging due to the inherent complexity of molecular data and the scarcity of high-quality expert annotations. To bridge this gap, we introduce Mol-R1, a novel framework designed to improve explainability and reasoning performance of R1-like Explicit Long-CoT reasoning LLMs in text-based molecule generation. Our approach begins with a high-quality reasoning dataset curated through Prior Regulation via In-context Distillation (PRID), a dedicated distillation strategy to effectively generate paired reasoning traces guided by prior regulations. Building upon this, we introduce MoIA, Molecular Iterative Adaptation, a sophisticated training strategy that iteratively combines Supervised Fine-tuning (SFT) with Reinforced Policy Optimization (RPO), tailored to boost the reasoning performance of R1-like reasoning models for molecule discovery. Finally, we examine the performance of Mol-R1 in the text-based molecule reasoning generation task, showing superior performance against existing baselines.

You Don't Need Pre-built Graphs for RAG: Retrieval Augmented Generation with Adaptive Reasoning Structures

Large language models (LLMs) often suffer from hallucination, generating factually incorrect statements when handling questions beyond their knowledge and perception. Retrieval-augmented generation (RAG) addresses this by retrieving query-relevant contexts from knowledge bases to support LLM reasoning. Recent advances leverage pre-constructed graphs to capture the relational connections among distributed documents, showing remarkable performance in complex tasks. However, existing Graph-based RAG (GraphRAG) methods rely on a costly process to transform the corpus into a graph, introducing overwhelming token cost and update latency. Moreover, real-world queries vary in type and complexity, requiring different logic structures for accurate reasoning. The pre-built graph may not align with these required structures, resulting in ineffective knowledge retrieval. To this end, we propose a \textbf{\underline{Logic}}-aware \textbf{\underline{R}}etrieval-\textbf{\underline{A}}ugmented \textbf{\underline{G}}eneration framework (\textbf{LogicRAG}) that dynamically extracts reasoning structures at inference time to guide adaptive retrieval without any pre-built graph. LogicRAG begins by decomposing the input query into a set of subproblems and constructing a directed acyclic graph (DAG) to model the logical dependencies among them. To support coherent multi-step reasoning, LogicRAG then linearizes the graph using topological sort, so that subproblems can be addressed in a logically consistent order. Besides, LogicRAG applies graph pruning to reduce redundant retrieval and uses context pruning to filter irrelevant context, significantly reducing the overall token cost. Extensive experiments demonstrate that LogicRAG achieves both superior performance and efficiency compared to state-of-the-art baselines.

LAG: Logic-Augmented Generation from a Cartesian Perspective

Large language models (LLMs) have demonstrated remarkable capabilities across a wide range of tasks, yet exhibit critical limitations in knowledge-intensive tasks, often generating hallucinations when faced with questions requiring specialized expertise. While retrieval-augmented generation (RAG) mitigates this by integrating external knowledge, it struggles with complex reasoning scenarios due to its reliance on direct semantic retrieval and lack of structured logical organization. Inspired by Cartesian principles from \textit{Discours de la m\'ethode}, this paper introduces Logic-Augmented Generation (LAG), a novel paradigm that reframes knowledge augmentation through systematic question decomposition and dependency-aware reasoning. Specifically, LAG first decomposes complex questions into atomic sub-questions ordered by logical dependencies. It then resolves these sequentially, using prior answers to guide context retrieval for subsequent sub-questions, ensuring stepwise grounding in logical chain. To prevent error propagation, LAG incorporates a logical termination mechanism that halts inference upon encountering unanswerable sub-questions and reduces wasted computation on excessive reasoning. Finally, it synthesizes all sub-resolutions to generate verified responses. Experiments on four benchmark datasets demonstrate that LAG significantly enhances reasoning robustness, reduces hallucination, and aligns LLM problem-solving with human cognition, offering a principled alternative to existing RAG systems.

Enhancing Large Language Models with Reliable Knowledge Graphs

Large Language Models (LLMs) have demonstrated remarkable capabilities in text generation and understanding, yet their reliance on implicit, unstructured knowledge often leads to factual inaccuracies and limited interpretability. Knowledge Graphs (KGs), with their structured, relational representations, offer a promising solution to ground LLMs in verified knowledge. However, their potential remains constrained by inherent noise, incompleteness, and the complexity of integrating their rigid structure with the flexible reasoning of LLMs. This thesis presents a systematic framework to address these limitations, advancing the reliability of KGs and their synergistic integration with LLMs through five interconnected contributions. This thesis addresses these challenges through a cohesive framework that enhances LLMs by refining and leveraging reliable KGs. First, we introduce contrastive error detection, a structure-based method to identify incorrect facts in KGs. This approach is extended by an attribute-aware framework that unifies structural and semantic signals for error correction. Next, we propose an inductive completion model that further refines KGs by completing the missing relationships in evolving KGs. Building on these refined KGs, KnowGPT integrates structured graph reasoning into LLMs through dynamic prompting, improving factual grounding. These contributions form a systematic pipeline (from error detection to LLM integration), demonstrating that reliable KGs significantly enhance the robustness, interpretability, and adaptability of LLMs.

Reliable Reasoning Path: Distilling Effective Guidance for LLM Reasoning with Knowledge Graphs

Large language models (LLMs) often struggle with knowledge-intensive tasks due to a lack of background knowledge and a tendency to hallucinate. To address these limitations, integrating knowledge graphs (KGs) with LLMs has been intensively studied. Existing KG-enhanced LLMs focus on supplementary factual knowledge, but still struggle with solving complex questions. We argue that refining the relationships among facts and organizing them into a logically consistent reasoning path is equally important as factual knowledge itself. Despite their potential, extracting reliable reasoning paths from KGs poses the following challenges: the complexity of graph structures and the existence of multiple generated paths, making it difficult to distinguish between useful and redundant ones. To tackle these challenges, we propose the RRP framework to mine the knowledge graph, which combines the semantic strengths of LLMs with structural information obtained through relation embedding and bidirectional distribution learning. Additionally, we introduce a rethinking module that evaluates and refines reasoning paths according to their significance. Experimental results on two public datasets show that RRP achieves state-of-the-art performance compared to existing baseline methods. Moreover, RRP can be easily integrated into various LLMs to enhance their reasoning abilities in a plug-and-play manner. By generating high-quality reasoning paths tailored to specific questions, RRP distills effective guidance for LLM reasoning.