arXiv:2606.28351v3 Announce Type: replace Abstract: Recent Hypergraph-based retrieval-augmented generation (HyperRAG) methods use hyper edges to connect multiple entities simultaneously, enabling more efficient multi-entity evidence organization than pairwise graph structures. However, existing HyperRAG methods often rely on LLM-generated summaries to construct hyperedges, which can introduce hallucinations while also incurring high indexing costs. In addition, during retrieval, existing methods typically rely on either one-hop neighbor expansion or PageRank diffusion. The former may miss useful multi-hop evidence, while the latter can suffer from uncontrolled propagation over excessive hub nodes, leading to semantic drift and noisy reasoning chains. To address these challenges, we propose HyperSU, a novel hypergraph-based RAG framework featuring semantic-unit hyperedges and clue guided bidirectional retrieval. During construction, HyperSU formulates hyperedge construction as an entity-aware minimum-description length (MDL) optimization problem, inducing source-grounded semantic-unit hyperedges that balance sentence-level semantic coherence and entity compactness. It then constructs a hypergraph by modeling each semantic unit as a hyperedge over its co-mentioned entities. During retrieval, HyperSU performs clue-guided bidirectional expansion over the semantic-unit hypergraph, enabling both multi-hop evidence discovery and evidence-anchored noise reduction. Experiments show that HyperSU consistently improves answer accuracy over standard, graph-based, and hypergraph-based RAG baselines, raising average accuracy on GraphRAG Bench by 5.5 points over the strongest baseline (68.7 vs. 63.2), with larger gains on reasoning intensive tasks, where the relative improvement reaches 14.1%.