Large language models (LLMs) are rapidly transforming various domains, including biomedicine and healthcare, and demonstrate remarkable potential from scientific research to new drug discovery. Graph-based retrieval-augmented generation (RAG) systems, as a useful application of LLMs, can improve contextual reasoning through structured entity and relationship identification from long-context knowledge, e.g. biomedical literature. Even though many advantages over naive RAGs, most of graph-based RAGs are computationally intensive, which limits their application to large-scale dataset. To address this issue, we introduce fastbmRAG, an fast graph-based RAG optimized for biomedical literature. Utilizing well organized structure of biomedical papers, fastbmRAG divides the construction of knowledge graph into two stages, first drafting graphs using abstracts; and second, refining them using main texts guided by vector-based entity linking, which minimizes redundancy and computational load. Our evaluations demonstrate that fastbmRAG is over 10x faster than existing graph-RAG tools and achieve superior coverage and accuracy to input knowledge. FastbmRAG provides a fast solution for quickly understanding, summarizing, and answering questions about biomedical literature on a large scale. FastbmRAG is public available in https://github.com/menggf/fastbmRAG.

Retrieval-Augmented Generation (RAG) improves factual accuracy by grounding responses in external knowledge. However, existing RAG methods either rely solely on text corpora and neglect structural knowledge, or build ad-hoc knowledge graphs (KGs) at high cost and low reliability. To address these issues, we propose KG-Infused RAG, a framework that incorporates pre-existing large-scale KGs into RAG and applies spreading activation to enhance both retrieval and generation. KG-Infused RAG directly performs spreading activation over external KGs to retrieve relevant structured knowledge, which is then used to expand queries and integrated with corpus passages, enabling interpretable and semantically grounded multi-source retrieval. We further improve KG-Infused RAG through preference learning on sampled key stages of the pipeline. Experiments on five QA benchmarks show that KG-Infused RAG consistently outperforms vanilla RAG (by 3.9% to 17.8%). Compared with KG-based approaches such as GraphRAG and LightRAG, our method obtains structured knowledge at lower cost while achieving superior performance. Additionally, integrating KG-Infused RAG with Self-RAG and DeepNote yields further gains, demonstrating its effectiveness and versatility as a plug-and-play enhancement module for corpus-based RAG methods.

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

In the past two years, large language model (LLM)-based chatbots, such as ChatGPT, have revolutionized various domains by enabling diverse task completion and question-answering capabilities. However, their application in scientific research remains constrained by challenges such as hallucinations, limited domain-specific knowledge, and lack of explainability or traceability for the response. Graph-based Retrieval-Augmented Generation (GraphRAG) has emerged as a promising approach to improving chatbot reliability by integrating domain-specific contextual information before response generation, addressing some limitations of standard LLMs. Despite its potential, there are only limited studies that evaluate GraphRAG on specific domains that require intensive knowledge, like Alzheimer's disease or other biomedical domains. In this paper, we assess the quality and traceability of two popular GraphRAG systems. We compile a database of 50 papers and 70 expert questions related to Alzheimer's disease, construct a GraphRAG knowledge base, and employ GPT-4o as the LLM for answering queries. We then compare the quality of responses generated by GraphRAG with those from a standard GPT-4o model. Additionally, we discuss and evaluate the traceability of several Retrieval-Augmented Generation (RAG) and GraphRAG systems. Finally, we provide an easy-to-use interface with a pre-built Alzheimer's disease database for researchers to test the performance of both standard RAG and GraphRAG.

Retrieval-Augmented Generation (RAG) enhances language models by incorporating external knowledge at inference time. However, graph-based RAG systems often suffer from structural overhead and imprecise retrieval: they require costly pipelines for entity linking and relation extraction, yet frequently return subgraphs filled with loosely related or tangential content. This stems from a fundamental flaw -- semantic similarity does not imply semantic relevance. We introduce SlimRAG, a lightweight framework for retrieval without graphs. SlimRAG replaces structure-heavy components with a simple yet effective entity-aware mechanism. At indexing time, it constructs a compact entity-to-chunk table based on semantic embeddings. At query time, it identifies salient entities, retrieves and scores associated chunks, and assembles a concise, contextually relevant input -- without graph traversal or edge construction. To quantify retrieval efficiency, we propose Relative Index Token Utilization (RITU), a metric measuring the compactness of retrieved content. Experiments across multiple QA benchmarks show that SlimRAG outperforms strong flat and graph-based baselines in accuracy while reducing index size and RITU (e.g., 16.31 vs. 56+), highlighting the value of structure-free, entity-centric context selection. The code will be released soon. https://github.com/continue-ai-company/SlimRAG

By retrieving contexts from knowledge graphs, graph-based retrieval-augmented generation (GraphRAG) enhances large language models (LLMs) to generate quality answers for user questions. Many GraphRAG methods have been proposed and reported inspiring performance in answer quality. However, we observe that the current answer evaluation framework for GraphRAG has two critical flaws, i.e., unrelated questions and evaluation biases, which may lead to biased or even wrong conclusions on performance. To tackle the two flaws, we propose an unbiased evaluation framework that uses graph-text-grounded question generation to produce questions that are more related to the underlying dataset and an unbiased evaluation procedure to eliminate the biases in LLM-based answer assessment. We apply our unbiased framework to evaluate 3 representative GraphRAG methods and find that their performance gains are much more moderate than reported previously. Although our evaluation framework may still have flaws, it calls for scientific evaluations to lay solid foundations for GraphRAG research.

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

While standard Retrieval-Augmented Generation (RAG) based on chunks, GraphRAG structures knowledge as graphs to leverage the relations among entities. However, previous GraphRAG methods are limited by binary relations: one edge in the graph only connects two entities, which cannot well model the n-ary relations among more than two entities that widely exist in reality. To address this limitation, we propose HyperGraphRAG, a novel hypergraph-based RAG method that represents n-ary relational facts via hyperedges, modeling the complicated n-ary relations in the real world. To retrieve and generate over hypergraphs, we introduce a complete pipeline with a hypergraph construction method, a hypergraph retrieval strategy, and a hypergraph-guided generation mechanism. Experiments across medicine, agriculture, computer science, and law demonstrate that HyperGraphRAG outperforms standard RAG and GraphRAG in accuracy and generation quality.

Multimodal reasoning in Large Language Models (LLMs) struggles with incomplete knowledge and hallucination artifacts, challenges that textual Knowledge Graphs (KGs) only partially mitigate due to their modality isolation. While Multimodal Knowledge Graphs (MMKGs) promise enhanced cross-modal understanding, their practical construction is impeded by semantic narrowness of manual text annotations and inherent noise in visual-semantic entity linkages. In this paper, we propose Vision-align-to-Language integrated Knowledge Graph (VaLiK), a novel approach for constructing MMKGs that enhances LLMs reasoning through cross-modal information supplementation. Specifically, we cascade pre-trained Vision-Language Models (VLMs) to align image features with text, transforming them into descriptions that encapsulate image-specific information. Furthermore, we developed a cross-modal similarity verification mechanism to quantify semantic consistency, effectively filtering out noise introduced during feature alignment. Even without manually annotated image captions, the refined descriptions alone suffice to construct the MMKG. Compared to conventional MMKGs construction paradigms, our approach achieves substantial storage efficiency gains while maintaining direct entity-to-image linkage capability. Experimental results on multimodal reasoning tasks demonstrate that LLMs augmented with VaLiK outperform previous state-of-the-art models. Our code is published at https://github.com/Wings-Of-Disaster/VaLiK.

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG