Reading Between the Chapters: A Graph-Free RAG Rebuilt With AI and Human Feedback

Retrieval-augmented generation (RAG) systems that answer questions from document collections face compounding difficulties when high-precision citations are required: flat chunking strategies sacrifice document structure, single-query formulations miss relevant passages through vocabulary mismatch, and single-pass inference produces stochastic answers that vary in both content and citation selection. We present KohakuRAG, a hierarchical RAG framework that preserves document structure through a four-level tree representation (document $\rightarrow$ section $\rightarrow$ paragraph $\rightarrow$ sentence) with bottom-up embedding aggregation, improves retrieval coverage through an LLM-powered query planner with cross-query reranking, and stabilizes answers through ensemble inference with abstention-aware voting. We evaluate on the WattBot 2025 Challenge, a benchmark requiring systems to answer technical questions from 32 documents with $\pm$0.1% numeric tolerance and exact source attribution. KohakuRAG achieves first place on both public and private leaderboards (final score 0.861), as the only team to maintain the top position across both evaluation partitions. Ablation studies reveal that prompt ordering (+80% relative), retry mechanisms (+69%), and ensemble voting with blank filtering (+1.2pp) each contribute substantially, while hierarchical dense retrieval alone matches hybrid sparse-dense approaches (BM25 adds only +3.1pp). We release KohakuRAG as open-source software at https://github.com/KohakuBlueleaf/KohakuRAG.

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.

Retrieval-augmented generation (RAG) grounds language models in external corpora. Agentic RAG enables iterative search, yet exposes the model to isolated chunks without document structure, making it difficult to distinguish relevant evidence from chunks that merely resemble the query. Structure-aware methods such as PageIndex navigate document structure but cannot scale to the structures of large corpora, which do not fit in the LLM context. Hence, they first commit to a single document using a document retriever and cannot recover from a wrong choice. We propose RIT-RAG (Retrieval-Induced Tree RAG), which combines content retrieval with structural navigation. Offline, RIT-RAG builds a tree for each document from its table of contents or sitemap. At query time, it retrieves a broad set of chunks and uses their positions to induce manageable sub-trees, potentially across multiple documents. An LLM agent navigates these sub-trees, selectively reads promising nodes, and reformulates queries when needed. Thus, retrieval proposes where to look, while the agent decides what to read. Across financial, scientific, and customer-support benchmarks, RIT-RAG achieves the highest answer accuracy among vanilla, graph-based, and agentic baselines. On EntQABench, our new benchmark of 2.84 million technical-documentation webpages, it improves accuracy by 6.8 to 11.4 points over the strongest baseline across three LLMs.