Graph-Based Retrieval Augmented Generation

Graph-based retrieval-augmented generation (RAG) is widely used for multimodal, cross-document question answering. However, building corpus-level graphs is expensive, slow to query, and difficult to maintain. We present TrioRAG, a graph-free multimodal framework that integrates evidence from three complementary signals: the question, the anchor image, and a VLM-enhanced query generated from both. Each signal retrieves independently over a shared multi-vector index of page text and page images, and the results are combined through late fusion. Further, we introduce AutoQA, a multimodal automotive benchmark whose questions are grounded in noisy, web-sourced images rather than clean document-sourced figures. Its questions require reasoning across manuals. We position it as a model-curated testbed rather than a human-validated gold standard. Across three benchmarks, TrioRAG matches or outperforms graph-based systems while reducing total cost and accelerating per-query inference by 1.6-2.3 times. By construction, AutoQA grounds its questions in out-of-corpus web images. In this setting image retrieval reaches only 19.3% document-level recall, while text-derived signals, especially the VLM-enhanced query, keep retrieval robust.

Large language models (LLMs) suffer from a long-tail deficit: culturally specific facts, particularly those concerning underrepresented regions such as Latin America, appear too rarely in pretraining corpora to be reliably memorized. Retrieval-Augmented Generation (RAG) addresses this by grounding generation in external text, but structured alternatives such as Knowledge Graphs (KGs) offer tighter control over what enters the context, along with potential gains in explainability and updatability. We benchmark Graph-RAG against standard RAG on LatamQA, a culturally grounded multiple-choice dataset spanning eight thematic categories. The graphs are built end-to-end from Wikipedia articles with KGGen, a recent open-domain extractor, without manual curation in our main setting. G-Retriever is competitive with RAG and reduces the error of the base LLM by 72% with a standard KG and 78% with a benchmark-aware variant, the gap to RAG narrowing further as the graph is oriented toward task-relevant content. The trained projection transfers zero-shot to Portuguese without target-language fine-tuning, indicating multilingual reach.

Graph-based retrieval-augmented generation (RAG) can help answer questions that require information from many documents. However, building a graph often requires many language-model calls during ingestion. It is therefore important to ask whether its quality gains justify the additional cost. We present EffiRAG, a graph-based RAG system designed to reduce this cost. It uses the graph to locate relevant passages and generates answers from the original text. This design preserves source information while keeping graph construction and query processing lightweight. We evaluate EffiRAG on UltraDomain, which contains 120 open-ended questions from four domains. Compared with LightRAG-hybrid, EffiRAG produces the preferred answer on 93 questions. LightRAG is preferred on 7, and the remaining 20 are splits. EffiRAG also reduces total system cost by 57 percent, from USD 0.952 to USD 0.408. The cost includes language-model calls during ingestion and querying. The advantage remains as the corpus grows. At 10 and 20 documents per domain, EffiRAG uses a lightweight, non-LLM filter to skip low-salience chunks. It remains preferred over LightRAG-hybrid. It costs 4.2 times and 4.5 times less, respectively. The comparisons identify different quality-cost trade-offs. Graph-based RAG systems should therefore be evaluated by both answer quality and cost. The results favor graph structure that locates and preserves source evidence.

Retrieval-Augmented Generation (RAG) has empowered Large Language Models (LLMs) to tackle knowledge-intensive tasks. However, navigating global, heterogeneous knowledge bases (large-scale knowledge graphs and text corpora) for complex reasoning remains a challenge. Existing methods typically employ reactive, graph-driven exploration strategies, which blindly follow graph topology without adapting to the question context or evolving exploration progress, and lack deep bidirectional synergy between graph and text. To address these limitations, we propose CoG (Cognition on Graph), a cognitive-inspired, training-free framework for adaptive knowledge exploration. Drawing inspiration from human problem-solving, CoG performs a continuous plan-explore-reflect cycle, where it proactively formulates investigation plans, performs dual-source retrieval, and dynamically reflects on progress to adjust strategies. Crucially, it establishes deep bidirectional synergy between structured graph and unstructured text, where entities extracted from text dynamically guide graph exploration to bridge knowledge gaps. Extensive experiments on seven multi-hop QA benchmarks demonstrate that CoG significantly outperforms state-of-the-art methods while achieving superior exploration efficiency. Our code and datasets are available at https://github.com/zhougengxian/CoG.

Graph Retrieval-Augmented Generation (GraphRAG) can connect evidence distributed across a corpus graph, but most systems use largely shared exploration procedures across queries. This creates a structural mismatch: direct facts may need compact local neighborhoods, comparisons need balanced coverage of multiple targets, and mediated questions may require deeper paths through weakly related connectors. We present Mosaic, a training-free framework that formulates GraphRAG retrieval as a per-query control problem. An LLM analyzer converts query-specific evidence requirements into a bounded policy over seed selection, graph traversal, stopping, and evidence selection, while the corpus graph, indexes, scoring functions, grounding procedure, and answer generator remain shared. On GraphRAG-Bench, Mosaic achieves query-weighted Answer Correctness of 76.97 on Medical and 64.33 on Novel, improving over the strongest previously reported overall results by 5.13 and 4.43 points. On Medical, it reaches 95.1 Evidence Recall and 86.1 Context Relevancy. Controlled comparisons on an identical graph and generator show that no fixed narrow, medium, or wide policy is consistently optimal; Mosaic improves by 9.96 points over the strongest canonical fixed policy. Relative to Fixed Wide, it evaluates 81.9% fewer paths and retains 47.2% fewer evidence items. Transfer experiments on HotpotQA, MuSiQue, and 2WikiMultiHopQA further show that the policy interface can be applied without benchmark-specific retriever training.

Graph-based retrieval can improve multi-hop question answering, but existing approaches often incur high query-time costs and produce diffuse, oversized contexts that reduce generation efficiency. We present LiteRAG, a graph-based retrieval method that replaces expensive retrieval-time LLM control with query-conditioned algorithmic exploration and reasoning-chain context construction. On DistComp, a benchmark for multi-hop retrieval over distributed-systems papers, LiteRAG attains the highest overall quality among the evaluated methods (0.798) while reducing per-query latency by over 100$\times$ and cost by over 99% relative to GraphRAG Global and DRIFT. On UltraDomain, it matches LinearRAG on overall quality while using about 14$\times$ fewer tokens. An ablation study indicates that LiteRAG's query-adaptive thresholding and community-aware hub penalization are the main drivers of its token-efficiency gains.

Retrieval-Augmented Generation (RAG) mitigates large language models (LLMs) hallucinations, yet conventional dense retrieval struggles with the complex reasoning paths of multi-hop question answering (QA). Graph-based RAG captures multi-step relationships but suffers from severe semantic drift and high online latency due to noisy global graph traversals. Thus, we propose ISO-RAG (ISOperimetric Retrieval-Augmented Generation), a geometry-aware RAG framework. By projecting the underlying knowledge graph into a hyperbolic Poincare ball to precompute node-wise isoperimetric profiles, ISO-RAG prunes spurious edges during retrieval, restricting the search space to a strictly localized subgraph. This topological purification regulates Personalized PageRank (PPR) diffusion driving the retrieval process, ensuring exact and low-latency convergence. Experiments on multi-hop QA benchmarks demonstrate that ISO-RAG outperforms state-of-the-art baselines by average absolute gains of 10.0% in retrieval recall and 4.3% in downstream exact match, achieving a superior accuracy-efficiency trade-off by fundamentally eliminating the latency bottleneck of global traversals. Our source code is available at https://github.com/ZaiizaiZHANG/ISO-RAG.

A central bottleneck in multi-hop Question Answering (QA) is that the granularity at which a question is expressed often differs from the granularity at which corpus evidence is retrievable. Existing methods address this mismatch by imposing fixed graph structures over the corpus, by iteratively reformulating the query, or by executing a generated program over it, but these strategies do not explicitly decide when a query unit is already supported by evidence and when it should be refined. We formulate this bottleneck as retrievable granularity discovery and introduce Hi-Q, an evidence-conditioned framework for hierarchical query refinement. At each query node, a resolution operator tests whether retrieved evidence supports the current query unit; resolved nodes terminate, while unresolved nodes are expanded by a dependency-preserving binary operator and checked by a semantic coverage verifier. Hi-Q therefore grows a query tree whose topology is determined by corpus support signals rather than by a fixed decomposition template or a pre-built graph. We evaluate Hi-Q on three multi-hop QA benchmarks, primarily under full-corpus retrieval, where dependent evidence must be located among open-domain distractors rather than within a small annotated pool. In this setting Hi-Q reaches 52.3 EM and 64.0 F1 averaged over the three benchmarks, ahead of the iterative retrieval baseline IRCoT by 15.1 EM / 18.2 F1 on that same average, and ahead of the graph-based RAG baseline PropRAG by 11.5 EM / 12.0 F1 on MuSiQue-full, without corpus-wide graph construction. In the restricted supporting/distractor setting used by prior work, Hi-Q likewise attains the best accuracy, with 57.9 EM and 69.3 F1 on average, ahead of PropRAG by 5.6 EM / 3.9 F1 and IRCoT by 13.7 EM / 15.8 F1. The project page is available at https://hi-q-project.github.io/.

Multi-hop question answering in retrieval-augmented gener?ation (RAG) often benefits from retrieving beyond the few candidates that will finally be read: narrow retrieval can miss an indispensable hop, while expanded retrieval introduces topical distractors. This challenge is not tied to a particu?lar knowledge-base format. Candidate pools may come from standalone retrievers, standard RAG backends, or graph-based retrieval pipelines. What is needed is a query-aware selection layer that can use relational structure to filter candidates be?fore generation. PAGE-RAG addresses this setting by using a graph as a temporary selection structure, rather than assum?ing a graph-structured knowledge base. It builds a query-local graph over retrieved candidates, records why candidates are connected, and treats each connection as a support hypothe?sis rather than support itself. We identify the resulting failure mode as a connectivity-support gap: connected candidates do not necessarily support the answer. We propose PAGE-RAG, a Provenance-Aware Graph Evidence promotion method that scores candidate paths with relevance, source-tracing meta?data, specificity, hubness, noise, and coherence signals, and applies minimal sufficient selection to promote supporting facts into a compact reader context. PAGE-RAG can serve as a complete retrieval-to-reading pipeline, and the same promo?tion stage can be inserted after existing retrieval or RAG sys?tems without replacing their upstream retrieval logic. Across three multi-hop QA benchmarks under the same final bud?get, PAGE-RAG improves support F1 and answer F1 by 10.4 and 3.3 points on a weighted average over a strong retriever. As a plug-in, PAGE-RAG further improves all reported RAG backends, including reasoning-oriented, compression-based, graph-based, and document/chunk-level systems.

When a security researcher publishes a report on a cyberattack, detection engineers are supposed to turn it into working detection rules. In practice, most automated attempts at this only extract the simplest clues from the report --- bad IP addresses, domain names, and file hashes --- and turn them into block lists. This is a weak strategy, because attackers can change these simple clues within hours or days, so the resulting detections stop working almost as soon as they are deployed. Security teams describe this idea with the Pyramid of Pain. This project asks whether feeding a report into a knowledge-graph retrieval system, Microsoft GraphRAG, rather than a standard vector-similarity retrieval system (Naive RAG), produces detection plans that rely more on these durable, top-of-pyramid clues. Both systems are given the same report, the same generation instructions, and the same language model to write the final plan; only the retrieval step differs. In a detailed case study of one APT28 report, the GraphRAG plan kept firing at 100% of its detections after every IP address, domain, and file hash in the report was rotated, while the Naive RAG plan kept firing at only 29%. Repeating the comparison across nine real CTI reports from four vendors confirms the same pattern: GraphRAG plans consistently reach higher, harder-to-evade levels of the pyramid, even when the two systems end up close on total score. The results support treating knowledge-graph-aware retrieval as the architecturally correct foundation for automatically generating SOC-deployable hunting plans, while showing that the wording of the generation prompt matters almost as much as the retrieval back-end itself.

While retrieval-augmented generation (RAG) has proven effective at giving LLMs access to external knowledge, mainstream dense-retrieval implementations remain inherently limited in handling structured constraints and multi-hop reasoning. Graph-based methods address this by constructing knowledge graphs offline, but they often fragment semantics, incur high maintenance, and complicate incremental updates. We propose SAG (SQL-Retrieval Augmented Generation), a structured retrieval architecture that organizes documents into an event-entity index without building a global knowledge graph. SAG represents each chunk as a semantically complete event paired with its entities, forming a latent hyperedge that preserves n-ary relations without decomposing them into triples. At query time, SAG treats shared entities as join keys to connect related chunks. This dynamically yields a query-scoped neighborhood of events, and yet every piece of evidence remains the original chunk throughout. Experiments on HotpotQA, 2WikiMultiHopQA, and MuSiQue show that SAG achieves the best retrieval and end-to-end QA performance on every benchmark, with gains that widen as reasoning-chain complexity increases. On MuSiQue, where multi-hop evidence chaining is most demanding, SAG reaches 80.36% Recall@5, outperforming the strongest baseline by 11.52 points. This work paves the way for knowledge infrastructure that enables LLM agents to retrieve and reason over continually growing organizational knowledge.

Recent Retrieval-Augmented Generation (RAG) systems increasingly combine vector retrieval with structured knowledge, such as Graph RAG and Filtered vector search. However, existing database architectures struggle to support such complex RAG workflows efficiently, as they rely on out-of-DB pipelines or in-DB non-native integration, leading to high overhead. This demo paper presents AkasicDB, a database system that natively supports such RAG workflows by jointly executing vector similarity search, graph traversal, and relational filtering within a single execution framework. AkasicDB extends our prior work, Chimera, with native vector support to enable such unified execution. Based on AkasicDB, we demonstrate the first native integration of Vector-Graph-Relational RAG, which we refer to as Omni RAG. Through an interactive chat-style demonstration, users execute and visualize Omni RAG queries, directly experiencing its superior retrieval and reasoning over vector-only approaches while observing the practical limitations of existing database architectures in supporting Omni RAG. A demonstration video is available at https://youtu.be/8d09_dtrEIM

Retrieval-Augmented Generation (RAG) is essential for enterprise knowledge question answering (QA), particularly in domains with complex product documentation like telecommunications. However, existing RAG approaches largely overlook the holistic integration of diverse retrieval strengths, leading to inaccurate domain routing, poor utilization of hierarchical document structures, and consequently limited reasoning capabilities over enterprise knowledge. To address these limitations, we present VDGR-RAG, which integrates vector retrieval, directory-driven reasoning, graph traversal, and iterative reflection in a unified framework for accurate enterprise knowledge QA. Specifically, VDGR-RAG is an agentic GraphRAG system that first constructs a Hierarchical Heterogeneous Knowledge Graph ($\text{H}^2$KG) from document chunks to preserve both hierarchical directory structures and semantic relationships, and then employs a set of atomic tools for knowledge retrieval that can be freely composed to navigate the $\text{H}^2$KG: (1) a directory-enhanced routing tool that uses table-of-contents (TOC) structures to route user queries to appropriate domain-specific $\text{H}^2$KGs; (2) a multi-route retrieval tool that combines vector search, TOC-based agentic search, and graph search for comprehensive knowledge retrieval; (3) a directory backtracking tool that corrects knowledge localization biases; and (4) a dynamic reflection tool that iteratively plans the next retrieval phase. We conduct extensive experiments on our enterprise product documents across four wireless domains (e.g., energy saving and fault management). Experimental results demonstrate that our method significantly outperforms a variety of RAG baselines in terms of both knowledge retrieval recall and QA accuracy.

LLM-based repository-level code generation aims to generate code using the context available in a software repository, requiring LLMs to reason over complex code dependencies. Due to limited context windows and insufficient repository-specific understanding, LLMs typically rely on retrieval-augmented generation (RAG) to incorporate relevant code. Early RAG approaches primarily employ similarity-based retrieval, which often fails to retrieve code snippets that the target function depends on. Recent work introduces graph-based retrieval to model such dependencies, but typically relies on manually designed rules and static global graphs, leading to limited flexibility and high construction and maintenance costs. In contrast, human developers collect helpful context by implicitly constructing a partial dependency graph and iteratively inspecting along it. Inspired by this behavior, we propose DyRetriever, an efficient context retrieval method via partial dependency graphs. DyRetriever uses an LLM to first select a set of entry-point functions and then perform multi-hop reasoning along the code dependency graph. During multi-hop reasoning, it uses the LLM's semantic understanding to validate whether a function can help generate the target function, eliminating manually designed rules and enabling flexibility across scenarios. Instead of statically constructing a global dependency graph, DyRetriever builds a partial graph on demand and discards it after use, reducing construction and maintenance costs. We integrate DyRetriever with a similarity-based code retriever to build DyCoder and evaluate it on CoderEval and DevEval. Experimental results show that DyCoder achieves relative Pass@1 improvements of 25.63% and 59.73% on CoderEval and DevEval, respectively, compared with existing RAG-based methods, while being 7.4x faster than baselines based on static dependency graph construction.

Answering complex questions over large document collections requires assembling complementary evidence across sections and documents. GraphRAG offers structured retrieval but typically uses fixed traversal, while agentic RAG operates over weakly structured interfaces. Our key insight is that agents should navigate document structure within and across documents rather than repeatedly search from scratch. We introduce DocNavRAG, which organizes document hierarchies and cross-region relations into a navigable graph, exposes graph operations for locating, navigating, expanding, and fetching, and maintains an evolving evidence state to guide retrieval until sufficient evidence is collected. Across four long- and multi-document QA benchmarks, DocNavRAG improves answer quality and context sufficiency over the strongest baseline by 7.8% and 17.7% on average.

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.

Reported verdicts on GraphRAG versus vector RAG disagree, and the evidence is typically tied to a single corpus, embedder, and judge -- and, we show, to where citation quality is measured. We present a triple-robustness analysis that holds a five-pipeline architecture matrix fixed and varies embedder (local e5-small vs. Azure text-embedding-3-small), corpus (DO-178C typed-edge requirements vs. Wikipedia paragraph chains via MuSiQue), and judge (paired GPT-5.4 x GPT-4.1 on both corpora), over 2x4,440 main-matrix runs, 600 cross-corpus runs, and over 5,000 faithfulness judgments. (C2a) GraphRAG's graph walk floods the context window at precision 0.12-0.23, but the synthesizer cites selectively at precision 0.48-0.65; scoring the retrieved set as the attribution set inverts the architecture ranking, which reconciles part of the disagreement in prior reports. (C1) Answer-level citation winners are corpus- and stratum-conditional but embedder-robust: GraphRAG ties vanilla on short-hop DO-178C queries and wins every MuSiQue stratum, while agentic pipelines lead only on 3+-hop requirements queries. (C2b) Faithfulness is corpus-conditional: on DO-178C it declines with hop distance (trend p<0.05 in three of four judge x embedder combinations); on Wikipedia chains neither judge shows a collapse. (C3) Single-judge LLM faithfulness is fragile to retrieval state: GPT-5.4's self-kappa across embedders is 0.137 (41% verdict change) against a same-day test-retest floor of 0.76, and re-judging frozen inputs eleven weeks later gives kappa <= 0.14 for both judges. A learned router on dense embeddings alone reaches macro-F1 0.86 on hop classification (C4). We argue that RAG architecture claims should be tested at this level of robustness -- including robustness to the citation-measurement point -- before they are trusted.

Retrieval-augmented generation (RAG) over knowledge graphs requires retrievers that can effectively capture both graph structure and semantic information. Recent approaches have explored graph neural network (GNN)-based retrievers to model graph topology in multi-hop reasoning tasks. In parallel, graph language models (GLMs) have emerged as a promising paradigm that integrates graph reasoning and the semantic capabilities of language models. In this work, we introduce a GLM-based retriever and investigate the comparative strengths of GLM-based, GNN-based, and traditional vector-search-based retrievers in single- and multi-hop RAG settings, and with a particular focus on transferability to unseen domains. Our findings suggest that finetuned GLM retrievers generalize better out of domain, achieving SOTA on two multi-hop benchmarks. On in-domain multi-hop QA datasets they remain comparable to prior work, with promising scaling as parameters and subgraph coverage increase. GNN-based retrievers achieve higher graph coverage with an efficient training setup, whereas the vector-search baseline excels at single-hop datasets.

Large language models (LLMs) have demonstrated strong capabilities in structured query generation, making them a natural choice for Text-to-SPARQL, which translates natural language questions into executable SPARQL queries over knowledge graphs. However, their initial outputs remain unreliable: generated queries may be executable yet semantically misaligned with input questions, leading to incorrect retrieval. To address this issue, we propose Generator-Gate-Corrector (GGC), a framework for reliable LLM-based Text-to-SPARQL generation. GGC first uses a Generator to produce an initial query, then applies a Gate to predict whether correction is needed, and finally invokes a Corrector only for selected high-risk queries. This selective correction mechanism avoids unnecessary modifications and reduces the risk of degrading originally correct queries. Experiments on MCQA show that GGC improves query-level accuracy from 90.23% to 98.33% while reducing inference overhead by 45% compared with correcting all generated queries. Ablation studies show that the Gate is robust across thresholds and that Corrector training data composition affects correction effectiveness and stability. Overall, the results demonstrate that selective correction enhances the accuracy, reliability, and efficiency of LLM-based text-to-SPARQL generation.

Retrieval-augmented generation (RAG) spans lexical and dense retrieval, graph-based indexing, and agentic search, but these paradigms are usually evaluated on different benchmarks at one corpus size, leaving their accuracy-cost scaling unclear. To bridge this gap, we present a controlled study that varies corpus size along 28 strictly nested tiers spanning roughly 450-fold, while holding questions and a fixed bedrock of relevant and adversarial documents unchanged. Under one reader model and one judging protocol, we measure official accuracy, construction and query tokens, and latency. The results reveal a scale-dependent crossover rather than an unconditional winner. File-System Agent leads at the smallest shared tiers, but its sequential exploration costs 39 times more query tokens at the bedrock and becomes less effective as the search space grows. Around 10 million corpus tokens, BM25 overtakes it and leads at every larger shared tier, with a margin approaching 20 points at full scale. BM25 also anchors the low-cost end of the Pareto frontier without LLM-based construction. Dense retrieval remains efficient but less accurate, whereas graph-based RAG encounters construction walls before deployment scale and its scalable variants remain below BM25 at shared tiers. Overall, corpus growth increasingly favors global candidate ranking: lexical retrieval is the strongest scalable default, while agentic reasoning works best after ranked discovery rather than in place of it.

Graph Neural Networks (GNNs) and Large Language Models (LLMs) have each advanced recommendation systems by modeling structural and semantic signals, respectively. However, integrating their complementary strengths remains challenging, particularly in sparse settings where maintaining semantic precision is critical. We propose TRWH (Text-driven Random Walk Heterogeneous Graph Neural Network), a novel framework that fuses LLM-generated textual profiles with heterogeneous graph structures through strategic random walk augmentation. TRWH consists of three core components: (1) Embedding Creation, which produces user and item representations using both Word2Vec and LLM-based profiling; (2) a Heterogeneous Graph Neural Network (HeteroGNN) that propagates information across multi-relational edges; and (3) Random Walk-based Path Construction, which enriches sparse graphs with second-order user-user and item-item links. Experiments on the Amazon-2023 Fashion (2M users, 825K items) and Beauty (631K users, 112K items) datasets demonstrate that TRWH achieves substantial performance gains over state-of-the-art methods, including 80.0% RMSE and 52.6% MAE reductions on Fashion, and 25.7% and 10.8% improvements on Beauty. Notably, while random walks improve performance with traditional embeddings, they can dilute the nuanced representations learned by LLMs, underscoring the importance of adaptive integration strategies.

Advancing multimodal retrieval-augmented generation (RAG) for complex document understanding presents a formidable dual dilemma of accuracy and efficiency, particularly in graph RAG. Processing structurally sparse yet visually dense layouts, such as extracting a tiny data marker from a financial chart, often incurs computationally prohibitive token overhead while still triggering catastrophic hallucination. However, multimodal Graph RAG pipelines rely on graph-construction stages that assume Vision-Language Models (VLMs) can resolve sparse semantics within high-density layouts. We challenge this assumption, revealing that forcing VLMs to localize visual evidence, interpret semantics, and extract relations triggers a "Visual Attention Sink," a mechanism driving catastrophic semantic loss, while full-page processing incurs massive computational overhead. Controlled interventions verify that this failure is boundary-driven rather than content-specific and that semantic anchoring mitigates it. To fundamentally correct this flawed paradigm, we introduce DeCoRAG, a multimodal Graph RAG pipeline that shifts knowledge processing from coupled visual-semantic reasoning to "Cognitive Decoupling." Rather than passively processing raw pixels, its graph-construction stage establishes a macroscopic Semantic Anchor to neutralize the attention sink. This anchor subsequently drives our Region-Aware Pruning and Cropping (RAP-Crop) mechanism, shifting the reasoning space from dense, noisy backgrounds to purified, intent-driven semantic clusters. The resulting graph supports hybrid retrieval and answer generation. Across complex document benchmarks, DeCoRAG improves the semantic pass rate by up to 12.5 percentage points over the strongest baseline and generalizes to DocVQA. RAP-Crop reduces offline graph-construction prompt tokens by 40.8% without sacrificing end-to-end accuracy.

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.

Multi-hop question answering requires coordinating relational and textual evidence across reasoning steps, a combination neither a text corpus nor a knowledge graph can supply alone. Prior work often emphasizes only part of this loop: graph-augmented RAG retrieves from a pre-built or query-updated graph, KGQA systems search within topic-centered subgraphs, and memory-augmented agents maintain evolving memories without continuously reconciling graph memory with textual context. We propose Co-E, a training-free system built around synchronized bidirectional graph-text working memory. A synchronization cycle consolidates textual memory, extracts relational triples into graph memory, and injects graph facts back into the generation context. Because both memories are maintained, they shape subsequent retrieval and generation. Evaluated on six multi-hop QA benchmarks, Co-E improves over comparable training-free open-backbone baselines and is competitive with larger or trained systems.

Hypergraph-based RAG systems surpass traditional graph-based approaches by organizing complex n-ary atomic facts among entities, rather than relying solely on binary relationships. Despite the advancements in multimodal large language models (MLLMs) with enhanced visual capabilities, current hypergraph-based RAG frameworks predominantly restrict knowledge retrieval and reconstruction to a unimodal, text-centric paradigm. This limitation prevents them from fully leveraging the powerful visual perception capabilities of modern MLLMs. To address this gap, we systematically explore the integration of hypergraph awareness in RAG systems through visual cues. By incorporating visual representations of hypergraphs into the RAG pipeline, we introduce VizRAG, the first RAG system to support visual hypergraph structure awareness. Experimental results demonstrate that VizRAG significantly outperforms strong baselines, validating the promising potential of hypergraph visualization as a novel approach for RAG systems.

Deploying large language models (LLMs) as personal assistants on mobile devices demands privacy, low latency, and offline availability, yet the computational cost of giant models clashes with strict edge-hardware budgets. We argue that this tension cannot be resolved by model compression alone; it requires decomposing on-device intelligence into complementary functional roles. We present SmartRAG, a fully on-device framework that organizes an intelligent assistant around four coordinated modules -- Perception, Memory, Focus, and Thinking. At the core of SmartRAG is EvoNER, a continually learnable named-entity recognizer that incrementally expands its label inventory through teacher-distilled updates, enabling the system to absorb previously unseen entity types without retraining the backbone LLM. Extracted knowledge is stored in MRGraph, a three-layer provenance-preserving knowledge graph, and retrieved at query time through a hybrid pipeline combining graph traversal, lexical matching, and dense semantic search. The on-device LLM is invoked only for high-value semantic operations -- labeling, planning, and answer synthesis -- keeping inference costs bounded. Experiments on four QA benchmarks (TriviaQA, Natural Questions, HotpotQA, MultiHopQA) show that SmartRAG with a quantized 1.7B-parameter backbone achieves multi-hop reasoning performance competitive with models up to 18$\times$ larger, while running entirely on commodity smartphones within practical memory and latency envelopes.

Retrieval-augmented generation (RAG) has emerged as a critical paradigm for grounding Multimodal Large Language Models (MLLMs) in external knowledge. Recent GraphRAG methods introduce structured entity-relation graphs to improve retrieval and reasoning. However, they remain limited by treating knowledge graphs as static data structures built offline and queried in a single pass. This static paradigm misaligns with the interactive, iterative nature of knowledge-intensive reasoning, creating three bottlenecks: (i) text-centric fragmentation that impedes cross-modal reasoning, (ii) frozen structures unable to incorporate new evidence or correct errors, and (iii) rigid single-pass retrieval without adaptive refinement. To overcome these limitations, we introduce EvoGraph-R1, a self-evolving GraphRAG framework that reconceptualizes knowledge graphs as dynamic environments shaped through agent interactions. We formulate retrieval as a Markov Decision Process (MDP) where the agent observes the graph state and executes actions to query (GraphRetrieve), expand (WebSearch), refine (GraphEdit), or terminate (Answer) the reasoning. These actions reshape the hypergraph structure and generate feedback signals that guide subsequent evolution. Through this closed loop, the hypergraph evolves by integrating new evidence, correcting errors, and refining structure to support multi-hop reasoning. Experiments on multimodal VQA and text QA benchmarks demonstrate substantial improvements over existing RAG baselines in accuracy, coverage, and traceability, establishing self-evolving knowledge graphs as a fundamental paradigm across modalities.

Graph retrieval-augmented generation (GraphRAG) enhances large language models with structured knowledge, yet existing systems construct knowledge graphs in a single extraction pass, producing noisy entities and brittle retrieval. RAGU, an open-source modular GraphRAG engine, addresses this by separating extraction from consolidation: entities and relations pass through two-stage typed extraction, DBSCAN-backed deduplication, LLM summarization, and Leiden community detection. A key insight motivates a compact extractor: the skills an in-pipeline LLM needs - comprehension, extraction, reasoning over context - are language skills that grow only weakly with model size, unlike factual world knowledge. Accordingly, we train Meno-Lite-0.1, a 7B model optimized for language skills, which outperforms Qwen2.5-32B on knowledge-graph construction (+12.5% relative harmonic mean) and matches it on English GraphRAG tasks. On GraphRAG-Bench (Medical), RAGU retrieves the most complete context at every factoid level (evidence recall up to 0.84 vs. $\leq$0.76) and overtakes HippoRAG2 on synthesis tasks; on multi-hop factoid QA, the apparent HippoRAG2 advantage is shown to be largely an answer-format artifact. RAGU is installable via \texttt{pip install graph_ragu}, runs on a single GPU, and is released under MIT. The source code is publicly available at https://github.com/RaguTeam/RAGU, and the Meno-Lite-0.1 model can be obtained from https://huggingface.co/bond005/meno-lite-0.1.

Retrieval-Augmented Generation (RAG) addresses the limitations of Large Language Models (LLMs) when providing responses to domain-specific questions. Graph-based RAG approaches, such as GraphRAG, enhance retrieval by capturing semantic relationships within knowledge graphs (KGs). While the FAIR principles (Findability, Accessibility, Interoperability, and Reusability) are becoming prevalent for scientific data management, especially in complex domains such as medicine, existing RAG approaches lack a structured FAIRification of the underlying knowledge resources. This lack limits their potential for FAIR information retrieval in these domains. To address this gap, we introduce FAIR GraphRAG, a novel framework that integrates FAIR Digital Objects (FDOs) as the fundamental units of a graph-based retrieval system. Each graph node represents an FDO that incorporates core data, metadata, persistent identifiers, and semantic links. We leverage LLMs to support schema construction and automated extraction of content and metadata from data sources. The framework was co-designed by physicians and computer scientists to ensure technical and clinical relevance. We apply FAIR GraphRAG to a biomedical dataset in gastroenterology, demonstrating its applicability to RNA-sequencing data. Beyond ensuring adherence to the FAIR principles, FAIR GraphRAG significantly improves question answering accuracy, coverage, and explainability, particularly for complex queries involving metadata and ontology links. This work shows the feasibility of combining FAIR data practices with graph-based retrieval techniques. We see potential for applying our approach to other specialized fields such as education and business.

Multi-hop Question Answering over Knowledge Graphs faces a critical challenge: traditional retrieve-then-read pipelines break differentiability, preventing the retriever from learning to bridge the semantic gap where intermediate nodes lack lexical overlap with the query. To address this, we propose RSF-GLLM, a framework decoupling differentiable graph reasoning from answer generation. Our Recurrent Soft-Flow (RSF) module employs a GRU-guided query updater to propagate continuous relevance scores, utilizing a dynamic gating mechanism to traverse semantically dissimilar bridge nodes via structural cues. We introduce flow sparsity regularization to theoretically guarantee convergence from soft probabilities to discrete reasoning paths. These paths are extracted and textualized to fine-tune a Large Language Model (LLM), ensuring generation is grounded in factual topology. Experiments on WebQSP and CWQ demonstrate that RSF-GLLM achieves competitive performance with superior inference efficiency compared to LLM based computationally expensive approaches.

Knowledge graphs (KGs) that underpin Graph-based Retrieval-Augmented Generation (Graph-RAG) are increasingly built automatically by LLM-driven extraction rather than curated by experts. Proper evaluation would require instrumenting all pertinent stages: extraction, graph construction, and inference, coherently enough to localize failures, so that a failure at one stage is not discovered as a wrong answer at the end. We introduce TRIAGE, a stage-aware instrumentation framework for automated, document-grounded graph-RAG that asks not only whether the underlying graph can be trusted but at what cost it can be queried. TRIAGE attaches stage-specific, independently interpretable metrics to three stages: the KG Implementation (triple confidence, source coverage, and schema and canonicalization checks), the KG Validation by expert (graph-level structural quality, with correctness and completeness computed only as offline calibration when a reference is available), and the KG Usage (retrieval coverage, faithfulness, and retrieval cost); the deployed metrics need no gold annotations, the gold-requiring ones serving only as offline calibration. At usage time these metrics form a diagnostic chain of necessary conditions whose first broken link localizes the failure, and the diagnosis maps to the stage levers that can remedy it: extraction, graph and schema, or retrieval. TRIAGE is a theoretical framework with a proof of concept and a reproducible evaluation protocol.

GraphRAG is an extension of retrieval-augmented generation (RAG) that supports large language models (LLMs) by referring to graph-structured data as external knowledge. While this technique ideally captures intricate relationships, it often struggles with graph representations for LLMs, particularly for frozen LLMs, due to the misalignment between graph-based and text-based latent features. We tackle this issue by introducing the {\it Adaptive-masking for Graph Embedding (AGE)}. AGE employs a Transformer in a mask-based self-supervised learning (SSL) approach. We designed the architecture similar to text embedding encoders, addressing the latent feature misalignment. In contrast to natural language texts, graphs are concise representations, and there exist {\it key nodes} that hold dominant contextual information, which are challenging to predict from their surroundings. Masking such key nodes leads to inefficiency in the SSL process. Therefore, AGE focuses on predicting nodes apart from key nodes, utilizing a learnable node sampler. Our experimental results indicate that AGE significantly improves approaches using non-parametric search component in GraphQA tasks, achieving superior accuracy across four benchmark datasets with distinct characteristics.

Retrieval-augmented generation built on knowledge graphs (Graph RAG) outperforms flat passage retrieval on multi-hop question answering by leveraging graph structure. In most existing systems, however, the question only sets the seed nodes; the subsequent traversal becomes "query-blind", depending solely on the graph structure. The exception is QAFD-RAG, which implements query-aware traversal via a flow-diffusion solver with combined edge re-weighting. This architecture requires loading the full graph into Python memory and an iterative solver with a variable number of iterations complicating integration with the graph database. We propose a spreading-activation method that achieves the same query-aware traversal with a single per-step semantic gate: the step weight is the cosine similarity between the candidate entity's description and the question, and the number of iterations is fixed. The whole retrieval procedure - seed mapping, propagation, top-K selection and context assembly - is expressed as a single Cypher query executed in one round-trip to Neo4j; the graph never leaves the database. On MuSiQue our method matches QAFD-RAG by exact match (32.80 vs 33.50) and outperforms the strongest purely-structural baseline in our comparison, HippoRAG, by 5.3 EM and 3.4 F1; on 2WikiMultiHopQA HippoRAG and QAFD-RAG retain an advantage due to their phrase-node architectures. An ablation with the gate disabled confirms that the gate is the source of a simultaneous F1 gain of 3.6 to 7.4 points and a retrieval-latency reduction by a factor of 1.5 to 4.9.

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.

Multimodal large language models (MLLMs) are widely applied to visual document understanding. However, comprehending long documents remains an issue by the limited context window. Though recent multimodal retrieval-augmented generation (MMRAG) can address this challenge by retrieving relevant pages. It still struggles with the visual question answering (VQA) requiring holistic comprehension of a document. To cope with this, knowledge graph (KG) that summarizes global knowledge of a document can provide an effective solution. However, most existing LLM-based KG construction methods handle only the language modality, leaving the automatic creation of multimodal KGs (MMKGs) for visually rich documents largely unexplored. In this paper, we introduce a multimodal graph-based RAG approach to tackle this problem. Existing LLM-based KG methods evaluate the QA performance relying on indirect evidence such as comprehensiveness, diversity, empowerment, and so on. The lack of annotated datasets for comprehensive document-level VQA poses a significant challenge to effective model evaluation. To overcome this limitation, we also introduce a new benchmark, DLVQA (document-level VQA), which provides reference summaries and corresponding supporting facts for global document-level questions. Experimental results show that our approach outperforms existing MMRAG or KG-based approaches on multi-hop QA/VQA benchmarks and DLVQA.

Retrieval-Augmented Generation (RAG) enhanced by Knowledge Graphs has shown promise in complex multi-hop reasoning tasks. However, existing graph-based retrieval methods typically rely on flat, undirected topologies. During the retrieval process, the probability flow often gets trapped in high-degree abstract concept nodes which we define as probability black holes'', leading to semantic drift and noise accumulation. To address this, we propose SemFlowRAG, a framework that reconstructs the flat retrieval space into a corpus-adaptive semantic gradient graph. This data-driven self-organization enables a hierarchical structure to emerge naturally from the data distribution, capturing the intrinsic semantic granularity of the corpus to suppress structural noise. By quantifying the semantic abstractness of entities through the embedding variance of their associated passages, we transform static undirected edges into directed semantic constraints. Furthermore, we design an abstractness-guided directed PageRank algorithm that forces the retrieval trajectory to follow a high-to-low semantic abstractness'' gradient. This mechanism ensures layer-by-layer evidence convergence, smoothly guiding the retrieval process from abstract concepts to specific document evidence. Extensive experiments on complex QA datasets demonstrate that SemFlowRAG effectively mitigates the ``probability black holes'' issue, outperforming existing baselines in both retrieval and downstream reasoning performance.

Retrieval-augmented generation (RAG) over knowledge graphs has emerged as a promising approach for grounding large language models, yet existing benchmarks largely overlook the challenges of retrieval in multimodal knowledge graph RAG (MKG-RAG). In practice, retrieval is a critical bottleneck: multimodal knowledge is heterogeneous, difficult to align across modalities, and often poorly served by retrievers designed for unstructured corpora. To address this gap, we introduce MKG-RAG-Bench, a cross-domain benchmark explicitly designed to evaluate retrieval in MKG-RAG. MKG-RAG-Bench is constructed from two multimodal knowledge graphs spanning general and medical domains, and includes carefully aligned question-answering datasets that support controlled evaluation of both retrieval and downstream generation. The benchmark is built using an LLM-based curation pipeline that filters low-utility knowledge, generates structurally grounded queries with exact supervision, and systematically covers diverse modality configurations. Through extensive experiments across representative retriever families and modality settings, we show that effective multimodal retrieval remains challenging yet crucial for end-to-end MKG-RAG performance, and that retrieval quality strongly determines generation outcomes. By isolating retrieval as a first-class evaluation target, MKG-RAG-Bench provides a principled foundation for diagnosing current limitations and advancing multimodal knowledge graph RAG systems.

Retrieval-Augmented Generation (RAG) has emerged as a paradigm for enhancing large language models (LLMs) with external knowledge, yet existing graph-based methods face a fundamental limitation: entity-centric and chunk-centric approaches operate on representations anchored to original text without true knowledge fusion. While entity-centric methods connect logically related content and chunk-centric methods preserve context, both retrieve information separately through similarity search, missing emergent understanding from their synthesis. In this paper, we propose HyGRAG, a hierarchical graph RAG framework that transcends source documents by addressing three core challenges: constructing summaries that genuinely integrate contextual and relational information, leveraging these synthesized representations to access emergent knowledge during retrieval, and efficiently updating hierarchical structures for dynamic corpora. Specifically, we design hierarchical index structures over hybrid graphs with both chunk and entity nodes, then iteratively cluster them and generate LLM-based summaries. Then, we design context and relation-aware retrieval that searches across all abstraction levels while expanding through community membership. Moreover, we enable dynamic knowledge update through attachment-based algorithms with only local re-summarization. Experimental results show that HyGRAG improves the average accuracy of multi-hop reasoning tasks by 9.7%, while maintaining reasonable efficiency.

Graph-based retrieval-augmented generation (GraphRAG) is effective for knowledge-intensive and multi-hop query tasks; however, many existing methods primarily seed entity-based graphs and rely on implicit semantic relevance propagation. This often (i) under-retrieves when user queries are abstract and semantically sparse at the entity level, and (ii) suffers from brittle multi-hop reasoning, where noisy activations can derail entity-to-entity transitions and corrupt the inferred relation chain, yielding unreliable conclusions. To this end, we propose \texttt{FlowRAG}, a semantic-aware retrieval framework that improves both semantic recall and explicit reasoning. Specifically, \texttt{FlowRAG} constructs a quad-level heterogeneous graph over passages, summaries, sentences, and entities, where summary nodes serve as a coarse semantic hub. At retrieval time, a dual-granularity activation module combines summary--query alignment with sentence-level matching to activate relevant entities under paraphrase and abstraction robustly. We then introduce a frequency-aware weighted flow module that routes relevance through entity--passage links weighted by within-passage term frequency, pruning noisy connections and extracting high-confidence reasoning paths as an explicit logic skeleton for generation. Extensive experiments show that \texttt{FlowRAG} obtains state-of-the-art performance on complex reasoning benchmarks.

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.

Retrieval-Augmented Generation (RAG) offers an effective approach for large language models to access external knowledge. However, existing methods rely on dense similarity retrieval and face inherent limitations in handling structured constraints and multi-hop reasoning. Incorporating knowledge graphs partially alleviates these issues, but at the cost of semantic fragmentation, high maintenance overhead, and difficult incremental updates. This paper introduces SAG (SQLRetrieval Augmented Generation), a structured architecture for retrieval and agent systems. Instead of pre-building a global static graph, SAG converts each chunk into one semantically complete event and a set of indexing entities, then uses SQL join queries to dynamically link events that share entities into local hyperedges,constructing, at query time, a dynamically instantiated local index structure. This design avoids the need for global graph rebuilding and ongoing maintenance; the system naturally supports incremental writes, concurrent processing, and continuous scaling through its reliance on standard database infrastructure. Across HotpotQA, 2WikiMultiHop, and MuSiQue, three standard multi-hop benchmarks,SAG achieves the best results on 8 out of 9 Recall@K metrics, reaching 80.0% Recall@5 on MuSiQue, the benchmark with the highest multi-hop reasoning demands.SAG has also been deployed at a production scale of hundreds of millions of data items, with online retrieval latency kept within seconds. Project site and code are available at https://github.com/Zleap-AI/SAG-Benchmark.

Large Language Models (LLMs) struggle to incorporate new knowledge without forgetting or costly retraining. We propose DYNA, a lightweight framework that augments a frozen LLM with a temporal knowledge graph where events are nodes and temporal relations are directed, timestamped edges. The graph serves as an external, updatable memory. At query time, DYNA retrieves relevant nodes via random walks and centrality measures, then augments the LLM's response. Evaluated on three temporal recall tasks, DYNA reduces catastrophic forgetting by ~7% compared to fine-tuning and improves temporal ordering by ~5% over standard RAG. Higher graph clustering coefficients correlate with better retrieval, showing that graph structure matters. Contributions: (1) episodic memory as temporal KG, (2) retraining-free LLM augmentation, (3) graph properties as predictors of retrieval performance.

Generating novel, feasible, and high-quality research ideas is an important yet challenging task in scientific discovery. Recent Large Language Model (LLM)-based methods often ground idea generation with retrieved literature, but the retrieved evidence is usually provided as flat text, such as titles, abstracts, or summaries. Such flat contexts may contain redundant or weakly relevant information, while making cross-paper relations among problems, methods, mechanisms, and findings difficult to identify and trace. To address this challenge, we propose Graph2Idea, a knowledge graph-guided framework for retrieval-augmented scientific idea generation.Graph2Idea first retrieves papers according to the input topic, transforms them into structured knowledge triples, and dynamically constructs a target-centered knowledge graph to make literature relations explicit. It then extracts compact graph-derived contexts that retain target-relevant relational evidence while reducing noisy textual input. Based on these contexts, a two-stage generation process first identifies promising research directions and then guides the LLM to synthesize candidate ideas from graph-grounded evidence. Experiments on a scientific idea generation benchmark show that Graph2Idea outperforms representative baselines under the automatic evaluation protocol. Compared with the strongest baseline scores, it improves Novelty from 0.45 to 0.52, Quality from 0.24 to 0.29, and Feasibility from 0.22 to 0.28. These results suggest that graph-structured evidence helps LLMs generate research ideas through more explicit, compact, and traceable recombination of prior scientific knowledge.

Retrieval-Augmented Generation (RAG) fails systematically on queries requiring structural reasoning over interconnected entities. We compare eight retrieval architectures for aerospace supply chain intelligence, progressing from text retrieval through graph traversal to graph computation. Using a 46-node knowledge graph with 64 typed edges, we evaluate 23 queries across 10 intent categories and demonstrate that five query classes are structurally unreachable for vector retrieval. Our central finding is the operator vocabulary thesis: the barrier to LLM-based graph reasoning is not model intelligence but the computational operators available as tools. An LLM Query Planner with 9 typed traversal primitives outperforms bespoke handlers (F1 = 0.632 vs. 0.472) while generalizing to unseen queries. Adding 6 graph computation tools, the LLM selectively adopts them for exactly the query categories where traversal fails. We also identify a measurement gap: entity-level F1 systematically underscores structural queries where comprehensive answers are correct.

Graph foundation models (GFMs) emerged as a dominant paradigm in graph representation learning by leveraging large-scale pre-training for cross-domain inference. However, the parameterized knowledge encoded within these models is insufficient to cope with distribution shifts, limiting their generalization ability. To mitigate this issue, retrieval-augmented generation (RAG) has been introduced to incorporate external knowledge at inference time. Nevertheless, existing RAG frameworks operating in Euclidean space suffer from a fundamental geometric limitation: the polynomial volume growth of Euclidean space is inherently mismatched with the tree-structured external knowledge bases. This mismatch leads to the loss of semantic granularity in retrieval and gives rise to the hubness phenomenon.To address this limitation, we propose a Hyperbolic Retrieval-Augmented Generation (HyRAG) framework designed to enhance the generalization capabilities of GFMs. Specifically, the introduced Hyperbolic Knowledge Indexing module retains the tree-like hierarchies of the external knowledge base by modeling them within hyperbolic space. The Multi-granularity Retrieval module then provides GFMs with the global semantic anchors and local semantic nuances through coarse-grained and fine-grained knowledge retrieval, respectively. Finally, the Dual-path Fusion module achieves effective knowledge integration for graph tasks at both the feature and structural levels. Experiments on multiple graph benchmarks demonstrate significant improvements in the zero-shot setting, highlighting the generalization of our method for robust GFMs inference.

Document-grounded dialogue systems (DGDS) utilize knowledge from external documents to answer domain-specific user questions. Existing solutions typically divide documents into independent passages for retrieval and response generation. This approach, however, neither makes good use of structural information within documents nor provides enough (document) context for knowledge selection and responses. This paper proposes SF-Re2G to address such issues systematically. Firstly, we seek to improve a passage representation by contrasting it with others of the same section, thus improving the retrieval performance. Secondly, a structure-enhanced reranker is built, leveraging the fact that multiple grounding passages of one dialog turn tend to be in the same neighborhood. Specifically, candidates from the retrieval are grouped into subgraphs according to the document structure. The reranker will rescore the candidate integrating its group information. Finally, the chosen passages are used for responses, taking into account the subgraph context for better generation. Experimental results on two DGDS datasets validate our method for both Chinese and English.

Evaluating large language models (LLMs) across comprehensive benchmarks is expensive and time-consuming. We propose a graph-based prompt selection framework that models each benchmark as a similarity graph -- nodes are prompts connected if their embedding-space distance falls above a configurable threshold -- and applies Maximum Independent Set (MIS) algorithms to select a maximally diverse, non-redundant subset. We evaluate four MIS solvers (CPLEX, GREEDY, Online-MIS, ReduMIS) across six embedding models, three distance measures, six percentile thresholds, and four benchmarks (GPQA, IFEval, MMLU-Pro, Omni-MATH) covering 66 LLMs. Our central hypothesis -- that repeated selection under different random seeds yields consistent LLM rankings that may also differ from the full-benchmark baseline -- is strongly confirmed: Kendall's $W \geq 0.90$ in 99.2% of stochastic configurations (mean $W = 0.997 \pm 0.008$), while at higher percentile thresholds selected subsets achieve 25--48% prompt reduction on average. Ranking divergence from the full benchmark ($ρ< 0.95$) occurs in only 15.95% of configurations, concentrated at low thresholds ($p_{10}$--$p_{20}$) and benchmarks (GPQA, IFEval), identifying overly dense graphs as the primary failure mode.

Systematic characterization of drug-disease relationships is essential for drug discovery and repurposing, yet is hindered by the heterogeneity and rapid growth of biomedical literature. Existing datasets rely on labor-intensive curation and are often incomplete, while LLM-only approaches suffer from hallucination and weak evidence grounding. We introduce UniD$^3$, a unified framework that integrates Large Language Models with Knowledge Graph-enhanced Retrieval-Augmented Generation (KG-RAG) to extract, organize, and validate drug-disease knowledge across Drug-Disease Matching (DDM), Drug Effectiveness Assessment (DEA), and Drug-Target Analysis (DTA). UniD$^3$ processes 157,849 PubMed articles with Llama 3.3-70B and constructs knowledge graphs via a dual-stage strategy combining paper-level extraction with KG-level consolidation centered on drug and disease entities. These graphs support KG-RAG-based generation of structured datasets, evaluated through external benchmarks, fuzzy matching with curated resources, and clinician review. UniD$^3$ produces six knowledge graphs and large-scale datasets, including 28,915 DDM, 15,042 DEA, and over 4,000 DTA QA pairs. External validation shows strong performance (F1: 0.85-0.87 for DDM/DEA; 0.82 for DTA), with clinician review confirming high reliability (AUROC = 0.90). KG-RAG-augmented models outperform standalone LLMs, and the UniD$^3$ chatbot enables interpretable, citation-supported exploration of drug-disease relationships. UniD$^3$ provides a scalable, extensible framework for transforming unstructured biomedical literature into high-quality, structured drug-disease knowledge, supporting AI-driven discovery, repurposing, and precision medicine.

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.

Retrieval-augmented generation is intensively studied to ground large language models on external evidence. However, retrieving from a unified knowledge base could inevitably introduce irrelevant information that may mislead generation for complex reasoning. Inspired by the conditional computation of mixture of experts (MoE), where a router sparsely selects specialized experts alongside shared ones for each input, we propose \textbf{M}ixture \textbf{o}f experts for \textbf{G}raph-based Retrieval-Augmented Generation, i.e., \textbf{MoG}. It organizes knowledge into two core components: (i) diverse, always-accessible hub graphs that encode semantically and structurally central knowledge and provide contextual clues for expert activation, and (ii) sparsely activated expert graphs that contain domain-specific evidence. MoG first accesses hub graphs to identify general evidence and derive contextual clues. Then, a topology-aware router dynamically activates a limited set of expert graphs conditioned on the query, thereby confining retrieval to a focused evidence subspace. Extensive experiments on challenging benchmarks show that MoG consistently outperforms strong baselines, with over 20% relative improvement on MuSiQue. Our code is available in https://github.com/DEEP-PolyU/MoG.

Retrieval-Augmented Generation (RAG) enhances LLMs by grounding generation in query-relevant external evidence. Beyond unstructured text corpora, Graph RAG integrates knowledge graphs into the retrieval pipeline, enabling LLMs to access entities, relations, and multi-hop dependencies encoded in structured knowledge. However, the same structured knowledge that empowers Graph RAG also creates a new privacy attack surface. We demonstrate that Graph RAG systems can be turned into structural oracles: through adaptive black-box interactions, an adversary can elicit sufficient relational evidence to reconstruct substantial portions of the hidden knowledge graph. We propose a structure-oriented reconstruction framework that recovers targeted graphs from both local and global perspectives. Specifically, Depth-Wise Heuristic Search extracts fine-grained node attributes by recursively expanding entity-centered evidence, while Breadth-Wise Diffusion Search infers graph topology by propagating across relation-induced neighborhoods. Experiments on generic and healthcare scenarios demonstrate that our method can recover over 90% of the original knowledge graph from representative Graph RAG systems, revealing sensitive entities, relations, and structural dependencies with high fidelity. Existing guradrails provide limited defense against our attack, highlighting the inherent difficulty of safeguarding structural privacy in Graph RAG pipelines.

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 extends retrieval-augmented generation by organizing corpora as explicit knowledge graphs, enabling graph-based retrieval for complex question answering. However, existing frameworks extract entities and relations within individual chunks, leaving cross-chunk relations -- those whose evidence spans multiple passages -- systematically absent from the index. Exhaustive LLM-based recovery of such relations is impractical due to the combinatorial explosion of chunk combinations. We present CrossAug, a GNN-guided CROSS-Chunk Graph AUGmentation method that enriches GraphRAG indices with cross-chunk relational structure as an offline step before query-time retrieval. CrossAug derives training supervision through self-supervised graph corruption, uses a topology-aware GNN to score subgraphs for missingness, and applies evidence-grounded LLM completion only to selected high-scoring regions. Experiments on three LLM-based GraphRAG frameworks across four multi-hop and long-document QA benchmarks demonstrate that CrossAug consistently improves performance, confirming the benefit of cross-chunk graph augmentation for retrieval-based question answering. Our code is available at https://github.com/DonFinliani/CrossAug.

Scientific diagrams are essential for communicating complex methodologies in academic papers. A natural way for researchers to specify such diagrams is through rough sketches, where text labels, connectors, and spatial arrangements express early semantic and topological intentions. However, sketches are usually incomplete, making them insufficient for directly producing publication-quality diagrams. Existing sketch-based generation methods mainly reconstruct the sketch itself, while recent text-driven diagram generation frameworks rely on textual semantics and do not fully exploit the topological structure contained in sketches. In this paper, we introduce DiagramRAG, a lightweight retrieval-augmented framework for sketch-based scientific diagram completion. Given a user sketch, DiagramRAG retrieves reference diagrams that are both semantically relevant to the sketch content and topologically compatible with its structure, and uses them to guide downstream diagram generation. To enable efficient structure-aware retrieval, we represent diagrams as knowledge graphs, synthesize sketch variants at different simplification levels, and train an embedding model to align sketches with compatible diagrams in a shared space. The retrieved references further provide content, topology, and visual priors for completing and rendering the final diagram. Experiments show that DiagramRAG achieves F1-scores of 0.848 and 0.802 on DiagramBank and FigureBench, respectively, and improves generation quality with the best VLM-as-a-Judge score of 7.170, while reducing inference latency to 35.48 seconds per sample. Our code and data are available at https://anonymous.4open.science/r/DiagramRAG-A262 and https://huggingface.co/datasets/anonymous-review-a262/DiagramSketch.

Large Language Models (LLMs) have been widely adopted in conversational applications. However, their reliance on parametric knowledge limits reliability in real-world scenarios that require dynamic or domain-specific information. Retrieval-Augmented Generation (RAG) addresses this limitation by incorporating external knowledge during generation, but existing text-based and graph-based RAG methods often struggle with noisy or irrelevant contexts. In this work, we propose Structure-aware Retrieval Augmented Generation (SA-RAG), which uses tables as an intermediate structured representation to provide a compact and controllable interface that reduces noise while preserving essential information. We introduce a quality-aware table metadata generation framework that models metadata normalization and effectiveness, improving metadata quality and downstream performance. Furthermore, we explore both training-free and training-based table generation methods. Generation validation and direct preference optimization further improve table quality while maintaining semantic and structural consistency. Experiments on two noisy real-world datasets show that SA-RAG significantly outperforms existing RAG baselines. Our code is publicly available at a public repository.

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.

Graph-based Retrieval Augmented Generation (GraphRAG) extends retrieval-augmented generation to support structured reasoning over complex corpora, but its reliability under resource-constrained, privacy-sensitive deployments remains unclear. In healthcare, where Electronic Health Record (EHR) data is complex and strictly regulated, reliance on cloud-based large language models (LLMs) introduces challenges in cost, latency, and compliance. In this work, we present a systematic evaluation of GraphRAG for EHR schema retrieval using locally deployed open-source LLMs. We implement the Microsoft GraphRAG pipeline on real-world EHR schema documentation and benchmark four models, including Llama 3.1 (8B), Mistral (7B), Qwen 2.5 (7B), and Phi-4-mini (3.8B), each deployed via Ollama on a single consumer GPU (8 GB VRAM). We evaluate indexing efficiency, knowledge graph construction, query latency, answer quality, and hallucination under both global and local retrieval modes. Our results reveal substantial differences: Llama 3.1 produces the richest knowledge graph (1,172 entities), Qwen 2.5 achieves the best answer quality (3.3/5), Phi-4-mini fails to complete the pipeline due to structured-output errors, and Mistral exhibits degenerate repetition behavior. We further show that GraphRAG exhibits a practical capacity threshold, where models below approximately 7B parameters fail to reliably produce valid structured outputs and cannot complete the pipeline. In addition, indexing and answer quality are decoupled across models, and local retrieval consistently outperforms global summarization in both latency and factual grounding, with reduced hallucination. These findings demonstrate that GraphRAG is feasible on consumer hardware while highlighting the importance of model selection and retrieval design for robust deployment in regulated settings.

Retrieval-Augmented Generation (RAG) has become foundational for grounding large language models in domain-specific corpora, yet conventional vector-based RAG systems are fundamentally limited in their ability to capture the structured, multi-entity relationships that underpin financial market analysis. This paper presents a comprehensive comparative study of a novel two-hop Graph-RAG architecture versus a standard vector-only baseline for cross-entity financial sentiment analysis. Our system constructs a sentiment-weighted knowledge graph of 59 equity entities from 255 news articles covering 10 major technology stocks, then augments dense retrieval with intensity-filtered graph traversal over INFLUENCES edges to surface relational evidence inaccessible to vector search alone. We evaluate both architectures on 100 grounded queries (30 Direct, 70 Relational) using semantic similarity, entity recall, RAGAS metrics, latency benchmarks, and ablation studies. Graph-RAG achieves a statistically significant improvement in entity recall (+6.4%, p < 0.001, Wilcoxon signed-rank) and delivers substantially more relevant answers for complex multi-entity queries (+11.7% Answer Relevancy), with gains concentrating in relational question types (+16.1%). Critically, these improvements come at no measurable cost to answer quality (delta = +0.001 semantic similarity, Cohen's d = 0.078), with a modest 22.6% increase in mean latency offset by an 80% reduction in latency variance. An ablation study on the graph traversal intensity threshold reveals an inverted-U relationship with answer quality, identifying tau = 0.5 as optimal over the production default of tau = 0.7. These findings characterize a precision-for-coverage trade-off inherent to graph-augmented retrieval and provide actionable architectural guidance for practitioners building RAG systems for multi-entity financial analysis.

Graph-structured retrieval-augmented generation (RAG) systems can improve answer quality on multi-hop questions, but many current systems rely on large language models (LLMs) to extract entities, relations, and summaries during indexing. These calls add token and wall-clock costs that grow with corpus size. We present ContextRAG, a graph RAG system whose graph topology is constructed without LLM-based entity or relation extraction. ContextRAG derives a fuzzy concept graph over chunk embeddings using residual-quantization k-means and Formal Concept Analysis with Lukasiewicz residuated logic. Bridge-like and meet-derived context nodes are induced by soft fuzzy join and meet operations, rather than by LLM-written graph edges. On a 130-task UltraDomain subset, ContextRAG builds its index with 30 LLM calls and 22,073 tokens. In contrast, a local HiRAG reproduction stress test required 870 indexing calls and 3.54M tokens on a 20-task subset before failing during graph construction; linear extrapolation to 130 tasks implies over 23M indexing tokens. ContextRAG obtains 33.6% F1 overall and 36.8% F1 on multi-hop tasks. An activation analysis shows that queries retrieving at least one lattice-derived node in the top five achieve +3.9 percentage points F1 over queries that do not; this association is diagnostic rather than causal.

Retrieval-Augmented Generation can improve factuality by grounding answers in external evidence, but Agentic GraphRAG complicates what it means for citations to be faithful. In these systems, an agent explores a knowledge graph before producing an answer and a small set of citations. We frame citation faithfulness as a trajectory-level problem: final citations should not only support the answer, but also account for the graph traversal, structure, and visited-but-uncited entities that may influence it. Through controlled ablation experiments, we compare the effects of isolating, removing, and masking cited and uncited graph entities. Our results show that cited evidence is often necessary, as removing it substantially changes answers and reduces accuracy. However, citations are not sufficient, because accurate answers can also depend on uncited traversal context and surrounding graph structure. These findings suggest that citation evaluation in Agentic GraphRAG should move beyond source support toward provenance over the broader retrieval trajectory.