new

Get trending papers in your email inbox!

Subscribe

byAK and the research community

Mar 11

Medical Graph RAG: Towards Safe Medical Large Language Model via Graph Retrieval-Augmented Generation

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called MedGraphRAG, aimed at enhancing Large Language Model (LLM) capabilities and generating evidence-based results, thereby improving safety and reliability when handling private medical data. Our comprehensive pipeline begins with a hybrid static-semantic approach to document chunking, significantly improving context capture over traditional methods. Extracted entities are used to create a three-tier hierarchical graph structure, linking entities to foundational medical knowledge sourced from medical papers and dictionaries. These entities are then interconnected to form meta-graphs, which are merged based on semantic similarities to develop a comprehensive global graph. This structure supports precise information retrieval and response generation. The retrieval process employs a U-retrieve method to balance global awareness and indexing efficiency of the LLM. Our approach is validated through a comprehensive ablation study comparing various methods for document chunking, graph construction, and information retrieval. The results not only demonstrate that our hierarchical graph construction method consistently outperforms state-of-the-art models on multiple medical Q\&A benchmarks, but also confirms that the responses generated include source documentation, significantly enhancing the reliability of medical LLMs in practical applications. Code will be at: https://github.com/MedicineToken/Medical-Graph-RAG/tree/main

From Local to Global: A Graph RAG Approach to Query-Focused Summarization

The use of retrieval-augmented generation (RAG) to retrieve relevant information from an external knowledge source enables large language models (LLMs) to answer questions over private and/or previously unseen document collections. However, RAG fails on global questions directed at an entire text corpus, such as "What are the main themes in the dataset?", since this is inherently a query-focused summarization (QFS) task, rather than an explicit retrieval task. Prior QFS methods, meanwhile, fail to scale to the quantities of text indexed by typical RAG systems. To combine the strengths of these contrasting methods, we propose a Graph RAG approach to question answering over private text corpora that scales with both the generality of user questions and the quantity of source text to be indexed. Our approach uses an LLM to build a graph-based text index in two stages: first to derive an entity knowledge graph from the source documents, then to pregenerate community summaries for all groups of closely-related entities. Given a question, each community summary is used to generate a partial response, before all partial responses are again summarized in a final response to the user. For a class of global sensemaking questions over datasets in the 1 million token range, we show that Graph RAG leads to substantial improvements over a na\"ive RAG baseline for both the comprehensiveness and diversity of generated answers. An open-source, Python-based implementation of both global and local Graph RAG approaches is forthcoming at https://aka.ms/graphrag.

Estimating global article processing charges paid to six publishers for open access between 2019 and 2023

This study presents estimates of the global expenditure on article processing charges (APCs) paid to six publishers for open access between 2019 and 2023. APCs are fees charged for publishing in some fully open access journals (gold) and in subscription journals to make individual articles open access (hybrid). There is currently no way to systematically track institutional, national or global expenses for open access publishing due to a lack of transparency in APC prices, what articles they are paid for, or who pays them. We therefore curated and used an open dataset of annual APC list prices from Elsevier, Frontiers, MDPI, PLOS, Springer Nature, and Wiley in combination with the number of open access articles from these publishers indexed by OpenAlex to estimate that, globally, a total of \8.349 billion (8.968 billion in 2023 US dollars) were spent on APCs between 2019 and 2023. We estimate that in 2023 MDPI (\681.6 million), Elsevier (582.8 million) and Springer Nature (\546.6) generated the most revenue with APCs. After adjusting for inflation, we also show that annual spending almost tripled from 910.3 million in 2019 to \$2.538 billion in 2023, that hybrid exceed gold fees, and that the median APCs paid are higher than the median listed fees for both gold and hybrid. Our approach addresses major limitations in previous efforts to estimate APCs paid and offers much needed insight into an otherwise opaque aspect of the business of scholarly publishing. We call upon publishers to be more transparent about OA fees.

GS-LIVO: Real-Time LiDAR, Inertial, and Visual Multi-sensor Fused Odometry with Gaussian Mapping

In recent years, 3D Gaussian splatting (3D-GS) has emerged as a novel scene representation approach. However, existing vision-only 3D-GS methods often rely on hand-crafted heuristics for point-cloud densification and face challenges in handling occlusions and high GPU memory and computation consumption. LiDAR-Inertial-Visual (LIV) sensor configuration has demonstrated superior performance in localization and dense mapping by leveraging complementary sensing characteristics: rich texture information from cameras, precise geometric measurements from LiDAR, and high-frequency motion data from IMU. Inspired by this, we propose a novel real-time Gaussian-based simultaneous localization and mapping (SLAM) system. Our map system comprises a global Gaussian map and a sliding window of Gaussians, along with an IESKF-based odometry. The global Gaussian map consists of hash-indexed voxels organized in a recursive octree, effectively covering sparse spatial volumes while adapting to different levels of detail and scales. The Gaussian map is initialized through multi-sensor fusion and optimized with photometric gradients. Our system incrementally maintains a sliding window of Gaussians, significantly reducing GPU computation and memory consumption by only optimizing the map within the sliding window. Moreover, we implement a tightly coupled multi-sensor fusion odometry with an iterative error state Kalman filter (IESKF), leveraging real-time updating and rendering of the Gaussian map. Our system represents the first real-time Gaussian-based SLAM framework deployable on resource-constrained embedded systems, demonstrated on the NVIDIA Jetson Orin NX platform. The framework achieves real-time performance while maintaining robust multi-sensor fusion capabilities. All implementation algorithms, hardware designs, and CAD models will be publicly available.