Graph-Llm Joint

Hierarchical Graph Retrieval-Augmented Generation (GraphRAG) organizes corpus knowledge at multiple levels of granularity, yet fixed context construction may fail to translate these multi-resolution representations into a context suited to the current query. We identify this mismatch as the representation--inference gap. We propose Agentic Context Engineering for Hierarchical GraphRAG (ACE-GraphRAG), an inference-time context policy layer that supplements and adapts the initial context for generation. ACE-GraphRAG formulates context construction as a policy over gap-aware refinement, retrieval branches, and task-conditioned adaptation. Parallel Differential Retrieval acquires supplementary evidence from depth-oriented factual and breadth-oriented semantic branches. These evidence increments are consolidated with the initial context while preserving provenance and abstraction levels. Full-ACE applies the full policy uniformly within each task family, whereas Adaptive-ACE selects task- and topology-specific policies for individual queries. We evaluate ACE-GraphRAG on HotpotQA, 2WikiMultiHopQA, and four UltraDomain subsets across multi-hop QA and query-focused summarization. Full-ACE outperforms the evaluated RAG and GraphRAG baselines across both task families, while Adaptive-ACE further improves multi-hop QA and is preferred over Full-ACE on all four UltraDomain subsets. Ablation and topology analyses support treating context construction as a query- and task-dependent inference policy rather than a fixed procedure.

Question answering (QA) over complex documents requires models to retrieve and integrate evidence distributed across distant document regions and modalities. Multimodal GraphRAG provides a promising direction by organizing document evidence with graph structures. However, existing methods often suffer from unreliable cross-modal evidence indexing and expensive graph traversal. To address these issues, we propose HVM-GraphRAG, a holistic-view multimodal GraphRAG framework on complex document. HVM-GraphRAG uses a holistic view to guide graph construction, thereby reducing noisy and conflicting graph updates and building reliable indices between concept-level graph nodes and supporting multimodal chunks. During retrieval, HVM-GraphRAG searches over a compact concept-level graph and directly accesses supporting evidence through the constructed index, avoiding costly traversal over dense entity-level graphs. After obtaining the retrieved evidence, HVM-GraphRAG further reorganizes chunks into modality-specific groups, enabling the answering model to better integrate heterogeneous evidence. Experiments on three datasets show that HVM-GraphRAG achieves the best answer performance in most evaluated settings while substantially improving online retrieval efficiency over representative graph-based baselines.

Controllable video generation remains challenging due to the difficulty of specifying precise multi-object interactions using text prompts or motion-control inputs that primarily constrain pixel movement. In practice, trajectory-based control often requires users to draw accurate tracks for multiple objects, which scales poorly with scene complexity and becomes ambiguous under occlusion or overlap. To enable flexible yet precise multi-subject control, we introduce $\textbf{GraphVid}$, a graph-conditioned image-to-video generation model that enables interactive control through structured interaction graphs. We further curate $\textbf{GraphVid-Bench}$, a large-scale interaction-centric video dataset with structured relational annotations to enable training of interaction-aware video generation models. Despite using substantially less training data and fewer trainable parameters than prior motion-control methods, GraphVid delivers strong controllability and video quality. Compared with Motion-I2V, GraphVid reduces FID by up to 39.9% and FVD by 37.6%, while improving PSNR (9.87=>15.98) and SSIM (0.38=>0.61). Our results highlight the potential of structured semantic interfaces as a powerful paradigm for controllable video generation.

Retrieval-Augmented Generation (RAG) mitigates hallucinations in Large Language Models (LLMs) by grounding the generation process on external knowledge. However, standard RAG approaches struggle with multi-hop reasoning. While recent graph-based RAG methods improve the retrieval of interconnected chunks, they often rely on computationally expensive and error-prone LLM-based extraction pipelines. To address these issues, we propose TIGRAG (Token-Induced GraphRAG), an efficient graph-augmented RAG framework based on a token co-occurrence Knowledge Graph. TIGRAG directly models topological relationships between tokens using sliding-window co-occurrence statistics, thus enabling scalable graph construction. During inference, it combines graph-based semantic expansion and neural reranking to retrieve interconnected evidence for multi-hop reasoning. Specifically, it introduces an iterative entity-driven retrieval strategy that progressively expands the query using bridging entities extracted from previously retrieved contexts. We evaluated TIGRAG on three widely adopted multi-hop Question Answering (QA) benchmarks. Experimental results demonstrated that our framework consistently outperforms dense retrieval and graph-based RAG methods in both retrieval and downstream QA tasks, while substantially reducing indexing time, inference latency, and prompt footprint.

Graphs are widely used to model relational systems, with applications in domains such as social networks, finance, and biomedicine. Graph neural networks (GNNs) have become a mainstream approach for learning graph representations. With the rise of large language models (LLMs), recent studies have attempted to combine GNNs with LLMs. However, most existing works concentrate on node-level and edge-level tasks, while graph-level tasks, which require capturing more complex structural and feature information, remain relatively underexplored. Moreover, graph pretraining is a widely adopted strategy to alleviate the challenge of label scarcity. Most existing approaches are designed solely for GNNs such as GraphCL, leaving LLMs uninvolved in the process. To address these limitations, we propose GLIP, a Graph-LLM JoInt Pretraining framework for graph-level tasks. GLIP first performs graph augmentation to construct positive and negative pairs and introduces a multi-token selection strategy to identify patches informative in both structure and features. It further leverages a diffusion-based projector to enrich them with contextual information, enabling GLIP to capture signals from both global and local perspectives. Finally, GLIP employs a joint objective that integrates the LLM's semantic judgments with a contrastive alignment loss, ensuring consistent supervision at both the semantic and structural levels. After pretraining, GLIP is fine-tuned with limited labeled data for downstream tasks, and extensive experiments show that it outperforms state-of-the-art methods on graph-level classification and reasoning tasks. Our source code is publicly available at https://anonymous.4open.science/r/GLIP.

As advanced RAG variants like GraphRAG and Agentic RAG emerge, one leading question is when and how to use them. Here, we introduce a framework for different RAG scenarios evaluation and comparison on semi-structured knowledge bases, including regular RAG, GraphRAG, Modular RAG and Agentic RAG. We provide implementation for 9 standardized RAG scenarios, and conduct experiments for a comprehensive comparison. These scenarios are designed for real use cases regarding data and domain restrictions, spanning from simple document-based retrieval to advanced features such as hybrid text-graph retrieval, integration with computed or pre-defined domain knowledge graphs, agentic multi-step planning, and agent-graph integration. Besides, we present a novel context engineering method for GraphRAG and Agentic RAG, addressing the context/memory overflow issues, efficiently managing text and graph retrievals with new representations and agentic loop design, leading to 19%-53% reduction on token usage. Moreover, further analysis identifies a retrieval-generation gap where expanded retrieval does not proportionally improve generation quality, suggesting retrieval-oriented metrics overstate advanced retrieval benefits. This work provides data-driven insights on when and how to use them for building production-ready intelligent RAG systems.

Hallucinations and opaque reasoning remain unacceptable failure modes for clinical LLMs. We present a production-grade GraphRAG stack that constrains answers to verifiable graph chain-of-thought paths in a heterogeneous, ~700K-node medical knowledge graph powering a fertility assistant. The core idea is targeted navigation: a directed Pruned Landmark Labeling (PLL) oracle provides exact distances for sub-millisecond feasibility checks and simple-path enumeration, while a lightweight AStarNet heuristic operates strictly within the PLL corridor to prioritize clinically plausible expansions. We score and pack a small, diverse set of paths (CUI/semantic-type overlap, length prior, provenance priors) to condition generation, yielding compact prompts and improved Time to First Token (TTFT). On fertility-focused queries, the hybrid (PLL+AStarNet) establishes a better latency/recall Pareto frontier than text-only RAG and single-component baselines, lowers TTFT, and reduces clinician-audited hallucinations while preserving explanation clarity. The result is a practical recipe for explainable, low-hallucination multi-hop medical reasoning ready for real-world deployment.

Agentic GraphRAG trains language-model agents to iteratively retrieve and reason over graph-structured evidence, enabling more accurate and context-aware decision-making by efficiently navigating complex information networks. However, outcome-only reinforcement learning suffers from \textit{\textbf{answer-path reward aliasing}}, where correct answers may come from shortcuts rather than useful evidence paths. It also exhibits \textit{\textbf{search-update ambiguity}}, as scalar trajectory-level feedback does not indicate which retrieval actions to adjust. To mitigate these shortcomings, we present PathRouter, a path-aware training framework for agentic GraphRAG. PathRouter jointly evaluates each trajectory along answer correctness and evidence-path overlap, yielding four trajectory categories with differentiated GRPO advantage scaling that suppresses shortcut reinforcement while preserving evidence-seeking behavior. For evidence-poor trajectories, a frozen gold-evidence teacher provides token-level KL guidance on reasoning and search-query tokens, excluding answer tokens to avoid direct response imitation. Experiments on six QA benchmarks across three model sizes show that PathRouter consistently improves answer F1 and evidence-path overlap, achieving average F1 gains of 3.1 on 3B and 4.9 on 7B models compared to a strong baseline.

Large Language Models (LLMs) have advanced rapidly, but their limitations in structured and multi-hop reasoning underscore the need for graph-native, synergistic artificial intelligence (AI) systems. Graph-structured data underpins critical applications across social, biological, financial, transportation, web, and knowledge domains, making it essential to understand how LLMs can leverage graph computation for grounded, context-rich inference. Three complementary synergies are emerging: LLMs augmented with graph computation for retrieval and reasoning; bidirectional integration between LLMs and knowledge graphs (KGs), where LLMs support KG construction and curation while KGs enforce semantic constraints and factual consistency; and AI agents strengthened by graph algorithms for planning, decision making, and multi-step reasoning. In parallel, LLMs introduce new capabilities for graph data management and graph machine learning (ML) through natural language interfaces and hybrid LLM-graph neural network (GNN) pipelines. This tutorial synthesizes the algorithms, systems, and design principles driving these converging directions, offering data science and data mining researchers a unified perspective on integrating LLMs, graph data management, graph mining, graph ML, and agentic computation into next-generation graph-native AI systems.

Retrieval-Augmented Generation (RAG) has become an essential method for mitigating hallucinations in Large Language Models (LLMs) by leveraging external knowledge. Although effective for simple queries, traditional RAG struggles with large-scale, unstructured corpora where information is highly fragmented. Graph-based RAG (GraphRAG) incorporates knowledge graphs to capture structural relationships, enabling more comprehensive retrieval for complex reasoning. However, existing GraphRAG methods rely on isolated, fragment-level extraction for graph construction, lacking a global perspective on the whole corpus. As a result, these methods frequently lead to thematically inconsistent, logically conflicting, and structurally fragmented graphs that degrade retrieval performance. In this paper, we propose MemGraphRAG, a novel framework that introduces a memory-based multi-agent system to ensure high-quality graph construction. Specifically, MemGraphRAG employs a collaborative society of agents supported by shared memory, which provides a unified global context throughout the extraction process. This mechanism allows agents to dynamically resolve logical conflicts and maintain structural connectivity throughout the corpus. Furthermore, we propose a memory-aware hierarchical retrieval algorithm tailored for the constructed graph. Extensive experiments on multiple benchmarks demonstrate that MemGraphRAG outperforms the state-of-the-art baseline models with comparable efficiency. Our code is available at https://github.com/XMUDeepLIT/MemGraphRAG.

Drug synergy prediction (DSP) aims to identify efficacious drug combinations under various cellular contexts with different targets. However, the continual emergence of novel compounds results in variations in molecular scaffolds and sizes, causing drug synergy data to exhibit out-of-distribution (O.O.D.) shifts with respect to topological structure. Existing works rely on in-distribution (I.D.) assumption, failing to handle the O.O.D. shifts. To solve this problem, we study out-of-distribution generalized drug synergy prediction through a graph large language model for the first time. Nevertheless, O.O.D. generalized DSP is highly non-trivial, posing several challenges: i) how to discover structurally relevant and irrelevant molecular representations with respect to cell targets; ii) how to find the optimal graph neural architectures that accurately calculate molecular representations; and iii) how to jointly leverage molecular structural and semantic information in LLMs. To address these challenges, we propose OOD-GraphLLM, a novel graphLLM framework which is able to accurately predict drug synergy under O.O.D. settings via jointly optimizing molecular graph representation and biomedical semantic language representations in a unified manner. Furthermore, we finetune DrugSyn-LLM, a biomedical LLM, and employ a retrieval-augmented biomedical instruction tuning strategy to align molecular topological information and molecular semantic information with language-based reasoning for O.O.D. generalized DSP. Both the source code (https://github.com/EkkoXiao/Bio-GraphLLM) and released model (https://mn.cs.tsinghua.edu.cn/bio-graphllm/) are publicly available, where users are allowed to download model resources and interactively use the system through a web interface.

Methods to represent literary texts as graphs or sequences of graphs mainly focus on representing character interactions, and often overlook another crucial aspect: the textual context in which characters interact. We introduce Dynamic Heterogeneous Character Networks (DHCNs), which organize long novels into temporally localized heterogeneous graphs that align characters with their textual contexts. We extract around 20,000 DHCNs from Project Gutenberg, and propose GraphLit, a self-supervised learning framework that learns rich literary representations through a masked graph autoencoder objective. Across a wide range of 12 character-related tasks, GraphLit improves over text-only, graph-only and prior hybrid baselines. Ablations over different kinds of dynamic graph structures and architectural elements show that grounding characters in their context is the main performance driver, while explicitly encoding narrative order and character relationships provide task-dependent improvements. Finally, we demonstrate the applicability of DHCNs and GraphLit for literary analysis by studying the link between narrative non-linearity and dynamic social features.

Graph-based Retrieval-Augmented Generation (GraphRAG) advances flat document retrieval by structuring knowledge as relational graphs, enabling more coherent and effective reasoning. However, applying it to specific domains like legal reasoning faces critical challenges. (i) Legal corpora are heterogeneous, containing multi-granular knowledge from cases, articles and interpretations. A flat knowledge graph cannot adequately differentiate between factual details, applied rules, and abstract principles, limiting accurate retrieval. (ii) Reliable legal judgment demands transparent, evidence-based reasoning. Traditional RAG passes retrieved context directly to an LLM without verification, resulting in opaque, error-prone reasoning. To this end, we propose LegalGraphRAG, a framework designed for reliable legal reasoning. Our approach introduces two core components: a hierarchical legal graph that hierarchically organizes legal sources to enable retrieval at appropriate abstraction levels, and a multi-agent system for reliable legal reasoning, where a Researcher retrieves candidate evidence, an Auditor rigorously verifies its validity against source documents, and an Adjudicator synthesizes the set of verified evidence to render a final judgment. Extensive experiments show that LegalGraphRAG achieves the state-of-the-art performance, outperforming existing GraphRAG baselines in accurate and trustworthy legal analysis. Our code, datasets and implementation details are available at https://github.com/XMUDeepLIT/LegalGraphRAG.

GraphRAG conditions language models on subgraphs retrieved from knowledge graphs, encoded via message-passing GNNs. Because these encoders entangle node contributions through iterated neighborhood aggregation, there is no closed-form way to determine how much each retrieved entity influenced the encoder's output, and therefore no way to faithfully audit what structural evidence actually reached the model. We introduce Ex-GraphRAG, which replaces the GNN encoder with a Multivariate Graph Neural Additive Network (M-GNAN), an extension of additive graph models to high-dimensional embedding spaces that yields an exact decomposition of the encoder's output across individual nodes and feature groups, without post-hoc approximation. On STaRK-Prime, this auditable encoder matches black-box performance. Using it to audit evidence routing, we uncover a semantic-structural mismatch: the nodes that dominate the encoder's output are structurally disconnected in the retrieved subgraph, held together by low-attribution intermediaries whose removal degrades multi-hop QA by up to 28%. This mismatch, invisible to any opaque encoder, reveals that semantic importance and structural connectivity are governed by disjoint sets of nodes, with direct implications for retrieval pruning, context construction, and failure diagnosis in graph-augmented LLMs.

Generative AI, particularly Large Language Models, increasingly integrates graph-based representations to enhance reasoning, retrieval, and structured decision-making. Despite rapid advances, there remains limited clarity regarding when, why, where, and what types of graph-LLM integrations are most appropriate across applications. This survey provides a concise, structured overview of the design choices underlying the integration of graphs with LLMs. We categorize existing methods based on their purpose (reasoning, retrieval, generation, recommendation), graph modality (knowledge graphs, scene graphs, interaction graphs, causal graphs, dependency graphs), and integration strategies (prompting, augmentation, training, or agent-based use). By mapping representative works across domains such as cybersecurity, healthcare, materials science, finance, robotics, and multimodal environments, we highlight the strengths, limitations, and best-fit scenarios for each technique. This survey aims to offer researchers a practical guide for selecting the most suitable graph-LLM approach depending on task requirements, data characteristics, and reasoning complexity.