# HARMON-E: Hierarchical Agentic Reasoning for Multimodal Oncology Notes to Extract Structured Data

arXiv: https://arxiv.org/abs/2512.19864 · HTML: https://mlsanity.com/paper/2512.19864/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 16 of its 58 references that are in the map.
- First posted on arXiv 22 Dec 2025.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 16 of 16)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining](https://mlsanity.com/paper/2005.02799/) (2020)
- [Natural Language Processing for EHR-Based Computational Phenotyping](https://mlsanity.com/paper/1806.04820/) (2018)
- [Data-to-Dashboard: Multi-Agent LLM Framework for Insightful Visualization in Enterprise Analytics](https://mlsanity.com/paper/2505.23695/) (2025)
- [Universal Abstraction: Harnessing Frontier Models to Structure Real-World Data at Scale](https://mlsanity.com/paper/2502.00943/) (2025)
- [LLMD: A Large Language Model for Interpreting Longitudinal Medical Records](https://mlsanity.com/paper/2410.12860/) (2024)
- [A Semi-Supervised Machine Learning Approach to Detecting Recurrent Metastatic Breast Cancer Cases Using Linked Cancer Registry and Electronic Medical Record Data](https://mlsanity.com/paper/1901.05958/) (2019)

## Built on by (most cited first, 2 of 2)

- [Configurable Clinical Information Extraction with Agentic RAG: What Works, What Breaks, and Why](https://mlsanity.com/paper/2606.19602/) (2026)
- [Towards Reliable AI Data Scientists: Data Agents with Workflow Harnesses](https://mlsanity.com/paper/2609.35255/) (2026)

## Abstract (arXiv)

Unstructured notes within the electronic health record (EHR) contain rich clinical information vital for cancer treatment decision making and research, yet reliably extracting structured oncology data remains challenging due to extensive variability, specialized terminology, and inconsistent document formats. Manual abstraction, although accurate, is prohibitively costly and unscalable. Existing automated approaches typically address narrow scenarios - either using synthetic datasets, restricting focus to document-level extraction, or isolating specific clinical variables (e.g., staging, biomarkers, histology) - and do not adequately handle patient-level synthesis across the large number of clinical documents containing contradictory information. In this study, we propose an agentic framework that systematically decomposes complex oncology data extraction into modular, adaptive tasks. Specifically, we use large language models (LLMs) as reasoning agents, equipped with context-sensitive retrieval and iterative synthesis capabilities, to exhaustively and comprehensively extract structured clinical variables from real-world oncology notes. Evaluated on a large-scale dataset of over 400,000 unstructured clinical notes and scanned PDF reports spanning 2,250 cancer patients, our method achieves an average F1-score of 0.93, with 100 out of 103 oncology-specific clinical variables exceeding 0.85, and critical variables (e.g., biomarkers and medications) surpassing 0.95. Moreover, integration of the agentic system into a data curation workflow resulted in 0.94 direct manual approval rate, significantly reducing annotation costs. To our knowledge, this constitutes the first exhaustive, end-to-end application of LLM-based agents for structured oncology data extraction at scale