EidosDoc: Implicit Structure Encoding for Cost-Effective Semi-Structured Document QA

Semi-structured documents are ubiquitous in scientific reports, financial statements, and technical manuals. Question answering over such documents requires simultaneous understanding of text, tables, charts, and complex hierarchical layouts. Existing methods either rely on repeatedly calling large language models for structure parsing and retrieval, leading to high cost and large latency, or they flatten the document and lose layout and hierarchy information, sacrificing answer accuracy. To address this, we propose EidosDoc, a novel system that achieves state-of-the-art accuracy with minimal computational expense. Our approach introduces three core innovations. (1) An Implicit Structure Encoder trained via contrastive learning and a structure consistency loss. This module jointly embeds hierarchical relationships, spatial positions, and textual content into a dense vector space, capturing document structure holistically without the need for manually defined and error-prone constructions. (2) A Hybrid Retrieval Pipeline that leverages BM25, layout fingerprints, and a lightweight cross-encoder to perform high-precision retrieval entirely without invoking an LLM, drastically reducing cost and latency. (3) A Dynamic Evidence Expansion mechanism that adaptively retrieves spatially adjacent and structurally related evidence, overcoming the evidence omission common in fixed-path retrieval methods. We evaluate EidosDoc on four benchmarks, and comprehensive evaluations show that EidosDoc achieves a new state-of-the-art accuracy on the four benchmarks. Crucially, it does so with a 50 times reduction in cost and 4 times lower latency compared to the previous state-of-the-art Method. These results demonstrate that EidosDoc establishes a new optimal trade-off among accuracy, cost, and speed, offering a practical and scalable path for accurate semi-structured document analysis.