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

Semi-structured documents integrate diverse interleaved data elements (e.g., tables, charts, hierarchical paragraphs) arranged in various and often irregular layouts. These documents are widely observed across domains and account for a large portion of real-world data. However, existing methods struggle to support natural language question answering over these documents due to three main technical challenges: (1) The elements extracted by techniques like OCR are often fragmented and stripped of their original semantic context, making them inadequate for analysis. (2) Existing approaches lack effective representations to capture hierarchical structures within documents (e.g., associating tables with nested chapter titles) and to preserve layout-specific distinctions (e.g., differentiating sidebars from main content). (3) Answering questions often requires retrieving and aligning relevant information scattered across multiple regions or pages, such as linking a descriptive paragraph to table cells located elsewhere in the document. To address these issues, we propose MoDora, an LLM-powered system for semi-structured document analysis. First, we adopt a local-alignment aggregation strategy to convert OCR-parsed elements into layout-aware components, and conduct type-specific information extraction for components with hierarchical titles or non-text elements. Second, we design the Component-Correlation Tree (CCTree) to hierarchically organize components, explicitly modeling inter-component relations and layout distinctions through a bottom-up cascade summarization process. Finally, we propose a question-type-aware retrieval strategy that supports (1) layout-based grid partitioning for location-based retrieval and (2) LLM-guided pruning for semantic-based retrieval. Experiments show MoDora outperforms baselines by 5.97%-61.07% in accuracy. The code is at https://github.com/weAIDB/MoDora.

Leveraging large language models (LLMs) to analyze complex documents -- such as academic papers, technical manuals, and financial reports -- has emerged as a mainstream and critical task in both research and industry. In practice, users must first filter relevant documents from large collections and then conduct in-depth analysis (e.g. question answering) over the selected subset, yet existing systems flatten documents into plain-text chunks, discarding the rich hierarchical structures (sections, tables, figures, equations) and degrading downstream performance. We present DocMaster, a hierarchical structure-aware document analysis system. DocMaster parses documents into hierarchical document trees preserving original layouts and constructs a structure-aware semantic index that enables accurate document filtering and in-depth analysis. We demonstrate DocMaster through an interactive web interface that enables users to upload document collections, construct tree-based and multi-view semantic indices, filter relevant documents via natural-language conditions, and perform follow-up question answering over the filtered results. The source code, data, and demo are available at https://doc-master.github.io/.

Long-document question answering (QA) requires large language models (LLMs) to reason over evidence scattered across lengthy documents, where answers often depend on event order, section-level context, and cross-part evidence connections. Although retrieval-augmented generation (RAG) reduces the input context by retrieving relevant evidence, existing structured RAG methods still face three limitations: costly query-agnostic knowledge organization, insufficient use of original document structure, and no reuse of historical reasoning experience. To address these limitations, we propose DocTrace, a multi-agent RAG framework for long-document QA that supports query-triggered knowledge organization, document-structure-aware and experience-guided reasoning. DocTrace preserves document hierarchy with a lightweight document structural tree index, constructs agent-shared hypergraph-structured working memory on demand during reasoning, and stores successful reasoning plans in graph-structured experience memory for future reuse, enabling adaptive exploration across related long-document questions. Experiments on four long-document QA datasets show that DocTrace achieves the best performance on three datasets, surpassing the strongest baseline, ComoRAG, by up to 8.85% in F1 and 4.40% in EM, while reducing the overall computational cost by 53.32%