# Robust Hierarchical Structures for Agentic Document Analysis

arXiv: https://arxiv.org/abs/2609.33322 · HTML: https://mlsanity.com/paper/2609.33322/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Web, search, and research agents, one of 16 directions in LLM agents and tool use.
- Builds on 31 of its 87 references that are in the map.
- First posted on arXiv 27 Sep 2026.

## Placed in

- LLM agents and tool use / [Web, search, and research agents](https://mlsanity.com/agents/web-search-and-research-agents/)

## Builds on (most cited first, 30 of 31)

- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Judging LLM-as-a-Judge with MT-Bench and Chatbot Arena](https://mlsanity.com/paper/2306.05685/) (2023)
- [Lost in the Middle: How Language Models Use Long Contexts](https://mlsanity.com/paper/2307.03172/) (2023)
- [RAPTOR: Recursive Abstractive Processing for Tree-Organized Retrieval](https://mlsanity.com/paper/2401.18059/) (2024)
- [LayoutLMv3: Pre-training for Document AI with Unified Text and Image Masking](https://mlsanity.com/paper/2204.08387/) (2022)
- [PubLayNet: largest dataset ever for document layout analysis](https://mlsanity.com/paper/1908.07836/) (2019)
- [Nougat: Neural Optical Understanding for Academic Documents](https://mlsanity.com/paper/2308.13418/) (2023)
- [Distilling Knowledge from Reader to Retriever for Question Answering](https://mlsanity.com/paper/2012.04584/) (2020)
- [DocBank: A Benchmark Dataset for Document Layout Analysis](https://mlsanity.com/paper/2006.01038/) (2020)
- [ContractNLI: A Dataset for Document-level Natural Language Inference for Contracts](https://mlsanity.com/paper/2110.01799/) (2021)
- [DocLayNet: A Large Human-Annotated Dataset for Document-Layout Analysis](https://mlsanity.com/paper/2206.01062/) (2022)
- [Retrieval Augmented Generation or Long-Context LLMs? A Comprehensive Study and Hybrid Approach](https://mlsanity.com/paper/2407.16833/) (2024)
- [MinerU2.5: A Decoupled Vision-Language Model for Efficient High-Resolution Document Parsing](https://mlsanity.com/paper/2509.22186/) (2025)
- [Language Models Enable Simple Systems for Generating Structured Views of Heterogeneous Data Lakes](https://mlsanity.com/paper/2304.09433/) (2023)
- [StructRAG: Boosting Knowledge Intensive Reasoning of LLMs via Inference-time Hybrid Information Structurization](https://mlsanity.com/paper/2410.08815/) (2024)
- [SmolDocling: An ultra-compact vision-language model for end-to-end multi-modal document conversion](https://mlsanity.com/paper/2503.11576/) (2025)
- [DocETL: Agentic Query Rewriting and Evaluation for Complex Document Processing](https://mlsanity.com/paper/2410.12189/) (2024)
- [Text-to-Table: A New Way of Information Extraction](https://mlsanity.com/paper/2109.02707/) (2021)
- [Vision Grid Transformer for Document Layout Analysis](https://mlsanity.com/paper/2308.14978/) (2023)
- [Document Parsing Unveiled: Techniques, Challenges, and Prospects for Structured Information Extraction](https://mlsanity.com/paper/2410.21169/) (2024)
- [A Declarative System for Optimizing AI Workloads](https://mlsanity.com/paper/2405.14696/) (2024)
- [HRDoc: Dataset and Baseline Method Toward Hierarchical Reconstruction of Document Structures](https://mlsanity.com/paper/2303.13839/) (2023)
- [AgenticData: An Agentic Data Analytics System for Heterogeneous Data](https://mlsanity.com/paper/2508.05002/) (2025)
- [FinSage: A Multi-aspect RAG System for Financial Filings Question Answering](https://mlsanity.com/paper/2504.14493/) (2025)
- [BookRAG: A Hierarchical Structure-aware Index-based Approach for Retrieval-Augmented Generation on Complex Documents](https://mlsanity.com/paper/2512.03413/) (2025)
- [Detect-Order-Construct: A Tree Construction based Approach for Hierarchical Document Structure Analysis](https://mlsanity.com/paper/2401.11874/) (2024)
- [QUEST: Query Optimization in Unstructured Document Analysis](https://mlsanity.com/paper/2507.06515/) (2025)
- [GRACE: Reinforcement Learning for Grounded Response and Abstention under Contextual Evidence](https://mlsanity.com/paper/2601.04525/) (2026)
- [Capturing Logical Structure of Visually Structured Documents with Multimodal Transition Parser](https://mlsanity.com/paper/2105.00150/) (2021)
- [pdfQA: Diverse, Challenging, and Realistic Question Answering over PDFs](https://mlsanity.com/paper/2601.02285/) (2026)

## Abstract (arXiv)

Large Language Models (LLMs) enable us to better understand text documents, including PDFs and Word documents. However, LLMs, as well as more modern LLM agents, i.e., those with tool-calling abilities, typically treat such documents as plain text, ignoring the fact that they are often organized hierarchically into sections and subsections. Extracting this structure, while difficult, can improve efficiency and effectiveness for agents (and humans)---since only sections relevant to a given task need to be processed. Unfortunately, prior work on structure extraction provides no formal guarantees on how well the inferred structure matches the true one. Instead, we target a robust and compact variant that is feasible to infer and useful in practice. Robustness ensures that the text under each subsection header is a superset of the text under the same header in the true structure. Compactness seeks to minimize this superset, reducing agentic cost (or human cognitive load). We propose SHED, a two-stage workflow for inferring a robust and compact structure. The first stage is pluggable with an infinite family of approaches, each guaranteeing robustness for a specific document class. We theoretically characterize the document space using these classes and their hierarchical relationships. Empirically, SHED improves F-1 scores (measuring the robustness--compactness trade-off) by 13%--68% over non-LLM baselines and 9%--15% over expensive LLM-based approaches. Finally, we show how SHED-inferred structures are valuable for agentic document analysis: agents using SHED outperform baselines, achieving 3%--23% higher accuracy while being up to 10x cheaper.