A hierarchical attributed graph rag framework for biomedical literature retrieval

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Abstract
Despite rapid progress in retrieval-augmented generation (RAG), existing systems still struggle to retrieve both fine-grained entity-level evidence and higher-level abstract knowledge from biomedical literature. Graph-based RAG offers a promising alternative to flat retrieval, and hierarchical Graph RAG extends this idea by enabling coarse-to-fine retrieval across multiple levels of abstraction. Its effectiveness, however, depends on hierarchy construction choices, uneven community connectivity, and query-dependent layer choice. These challenges are particularly important in literature-derived biomedical graphs, where the hierarchy is constructed automatically from documents rather than specified in advance. We introduce HAGRAG, a hierarchical attributed Graph RAG framework for PubMed-derived diabetes literature. HAGRAG constructs multi-level attributed communities, summarises them across layers, indexes them using hierarchical navigable similarity search, and supports layer-aware filtering during retrieval. It further evaluates alternative community detection algorithms and layer-weighting strategies to determine how hierarchy design affects retrieval behaviour. Across comparisons with baseline systems, HAGRAG achieves the strongest overall performance, including accuracy of 0.80, relevancy of 1.00, recall of 0.54, and mean semantic similarity of 0.65. Answer quality is further assessed through NLI-based entailment checks and independent diabetes-clinician validation. The results show that Leiden produces the most coherent hierarchy, while retrieval quality remains sensitive to clustering and weighting choices. Overall, the findings show that effective hierarchical Graph RAG depends not only on graph augmentation, but on constructing, navigating, and weighting the hierarchy.

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