Upgrade the Retriever First: What an LLM Call per Chunk Buys in RAG

Retrieval-augmented generation systems increasingly rely on document-structure treatments: structure-aligned chunking, LLM-generated chunk contexts, heading-path metadata, and hierarchical two-stage retrieval. Separate studies support each on different corpora, embedders, and metrics, and none control for a shared confound: any text prepended to a chunk perturbs its embedding. We present a mechanism-isolating ablation testing all four treatments under one protocol, matching chunk sizes across conditions and adding a semantically null placebo---heading paths that are structurally valid but shuffled across documents. We score retrieval with a coverage-aware nDCG and test four pre-registered contrasts via document-clustered bootstrap with Holm correction, on two distant corpora: 200 Wikipedia Featured Articles (951 queries) and 1,585 QASPER papers (4,303 questions). Organization helps, and the cause is content, not tokens: structure-aligned chunks with real heading paths beat contextualized fixed windows (+0.022 / +0.012 cov-nDCG@10) and the placebo (+0.010 / +0.016). Naive two-stage hierarchical retrieval hurts (-0.033 / -0.015), traceable to first-stage section recall. Gold structure beats LLM-induced structure on Wikipedia but not on QASPER. Effects are small ($dz$ 0.06-0.11) but Holm-significant and consistent across corpora.

Retrieval-augmented generation (RAG) systems depend critically on how documents are chunked and searched. Fine-grained chunks can improve retrieval precision but expand the search space, increasing latency and cost; larger chunks reduce the number of candidates but make dense similarity less reliable, as the representation for each chunk mixes multiple topics and introduces more semantic noise. This trade-off becomes especially limiting in deep research tasks, where retrieval must be both fast and precise across large, heterogeneous corpora. We introduce MCompassRAG, a metadata-guided retrieval framework that uses topic-level signals as a semantic compass for selecting relevant evidence. Instead of relying only on cosine similarity between queries and noisy chunk embeddings, MCompassRAG enriches chunk representations with topic metadata in the same embedding space and trains a lightweight retriever through LLM-teacher distillation. At inference time, MCompassRAG performs topic-aware retrieval without additional LLM calls, improving both efficiency and evidence quality. Across six complex retrieval benchmarks, MCompassRAG improves information efficiency (IE) by 8.24% on average with over 5 times lower latency than the strongest efficient RAG baselines. Code is available on https://github.com/AmirAbaskohi/MCompassRAG.

Retrieval-Augmented Generation (RAG) systems over enterprise knowledge bases must ingest heterogeneous document formats -- PDFs, Word documents, presentations, and scans -- whose content is locked inside complex visual layouts, multi-column pages, and dense tables. Rule-based extraction and OCR destroy reading order, flatten tables, and lose heading hierarchy, while fully agentic chunking over extracted text incurs high token costs and hallucination risk. We present Document Retrieval-Aware Chunking (D-RAC), an extension of our Web Retrieval-Aware Chunking (W-RAC) framework to arbitrary document formats. D-RAC first normalizes any input document into PDF, exploiting the fact that virtually every format has a faithful, deterministic PDF rendering. A single multimodal LLM pass then converts rendered pages into retrieval-optimized Markdown -- rewriting tables as self-contained prose statements and preserving heading hierarchy -- after which chunking proceeds exactly as in W-RAC: deterministic parsing into ID-addressable units followed by lightweight LLM-based chunk planning over identifiers rather than text. Source text is never regenerated during chunking, preserving W-RAC's cost, determinism, and observability benefits while unlocking every renderable format as a first-class input. On the 236-document, 795-page PDF subset of the RAG-Multi-Corpus benchmark spanning five enterprise domains, D-RAC converts and chunks the entire corpus in 72 minutes with zero errors, producing 1,748 retrieval-ready chunks. Compared to agentic chunking with frontier LLMs, D-RAC reduces chunking-stage output tokens by 95.7%, cutting chunking cost by 77.8% (GPT-4.1 pricing) to 85.6% (Gemini 2.5 Pro pricing) and chunking time by 75%. D-RAC scales linearly to documents of 500+ pages.