# MoDora: Tree-Based Semi-Structured Document Analysis System

arXiv: https://arxiv.org/abs/2602.23061 · HTML: https://mlsanity.com/paper/2602.23061/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 20 of its 28 references that are in the map.
- First posted on arXiv 26 Feb 2026.

## Builds on (most cited first, 20 of 20)

- [Qwen3 Embedding: Advancing Text Embedding and Reranking Through Foundation Models](https://mlsanity.com/paper/2506.05176/) (2025)
- [Compositional Semantic Parsing on Semi-Structured Tables](https://mlsanity.com/paper/1508.00305/) (2015)
- [LayoutLMv3: Pre-training for Document AI with Unified Text and Image Masking](https://mlsanity.com/paper/2204.08387/) (2022)
- [LongBench v2: Towards Deeper Understanding and Reasoning on Realistic Long-context Multitasks](https://mlsanity.com/paper/2412.15204/) (2024)
- [Visual Transformers: Token-based Image Representation and Processing for Computer Vision](https://mlsanity.com/paper/2006.03677/) (2020)
- [Scene Text Visual Question Answering](https://mlsanity.com/paper/1905.13648/) (2019)
- [DocFormer: End-to-End Transformer for Document Understanding](https://mlsanity.com/paper/2106.11539/) (2021)
- [Unifying Vision, Text, and Layout for Universal Document Processing](https://mlsanity.com/paper/2212.02623/) (2022)
- [Document Understanding Dataset and Evaluation (DUDE)](https://mlsanity.com/paper/2305.08455/) (2023)
- [mPLUG-DocOwl2: High-resolution Compressing for OCR-free Multi-page Document Understanding](https://mlsanity.com/paper/2409.03420/) (2024)
- [Language Models Enable Simple Systems for Generating Structured Views of Heterogeneous Data Lakes](https://mlsanity.com/paper/2304.09433/) (2023)
- [M3DocRAG: Multi-modal Retrieval is What You Need for Multi-page Multi-document Understanding](https://mlsanity.com/paper/2411.04952/) (2024)
- [Hierarchical multimodal transformers for Multi-Page DocVQA](https://mlsanity.com/paper/2212.05935/) (2022)
- [A Systematic Survey of Text Summarization: From Statistical Methods to Large Language Models](https://mlsanity.com/paper/2406.11289/) (2024)
- [PDFTriage: Question Answering over Long, Structured Documents](https://mlsanity.com/paper/2309.08872/) (2023)
- [SV-RAG: LoRA-Contextualizing Adaptation of MLLMs for Long Document Understanding](https://mlsanity.com/paper/2411.01106/) (2024)
- [ST-Raptor: LLM-Powered Semi-Structured Table Question Answering](https://mlsanity.com/paper/2508.18190/) (2025)
- [QUEST: Query Optimization in Unstructured Document Analysis](https://mlsanity.com/paper/2507.06515/) (2025)
- [SuperRAG: Beyond RAG with Layout-Aware Graph Modeling](https://mlsanity.com/paper/2503.04790/) (2025)
- [Analyzing the Efficacy of an LLM-Only Approach for Image-based Document Question Answering](https://mlsanity.com/paper/2309.14389/) (2023)

## Built on by (most cited first, 3 of 3)

- [MinerU-Popo: Universal Post-Processing Model for Structured Document Parsing](https://mlsanity.com/paper/2605.24973/) (2026)
- [EidosDoc: Implicit Structure Encoding for Cost-Effective Semi-Structured Document QA](https://mlsanity.com/paper/2609.27784/) (2026)
- [VikingRAG: Accurate and Token-efficient Retrieval-augmented Generation over Structured Documents](https://mlsanity.com/paper/2609.11390/) (2026)

## Abstract (arXiv)

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.