# Prompt, Plan, Extract: Zero-Shot Agentic LLMs Workflows for Lung Pathology Extraction from Clinical Narratives

arXiv: https://arxiv.org/abs/2606.19852 · HTML: https://mlsanity.com/paper/2606.19852/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 19 references that are in the map.
- First posted on arXiv 18 Jun 2026.

## Builds on (most cited first, 10 of 10)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Gemma 3 Technical Report](https://mlsanity.com/paper/2503.19786/) (2025)
- [gpt-oss-120b & gpt-oss-20b Model Card](https://mlsanity.com/paper/2508.10925/) (2025)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [A Study of Generative Large Language Model for Medical Research and Healthcare](https://mlsanity.com/paper/2305.13523/) (2023)
- [UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition](https://mlsanity.com/paper/2308.03279/) (2023)
- [Clinical Relation Extraction Using Transformer-based Models](https://mlsanity.com/paper/2107.08957/) (2021)
- [Extracting Thyroid Nodules Characteristics from Ultrasound Reports Using Transformer-based Natural Language Processing Methods](https://mlsanity.com/paper/2304.00115/) (2023)
- [Entity Decomposition with Filtering: A Zero-Shot Clinical Named Entity Recognition Framework](https://mlsanity.com/paper/2407.04629/) (2024)

## Abstract (arXiv)

Information extraction from pathology reports is essential for cancer staging, tumor registry population. Yet key data remains embedded in narrative reports, making manual extraction labor-intensive and error-prone. Traditional supervised Natural Language Processing pipelines address this through fully supervised Named Entity Recognition and Relation Extraction, but require expensive manual annotation and suffer cascading failures when upstream entities are missed. In this study, we developed a zero-shot, agentic workflow, and evaluated five open-source generative Large Language Models (LLMs) to populate 13 College of American Pathologists synoptic fields from lung resection pathology reports. We compared them against a state-of-the-art supervised GatorTron NER-RE baseline using a novel, registry-aligned evaluation framework. The baseline achieved Micro-F1of 0.960, while the best zero-shot model (GPT-OSS-20B) achieved Micro-F1 of 0.893 (recall: 0.949), accurately extracting complex relations like Pathologic Stage without task-specific training. These results suggest that open-source, zero-shot agentic LLMs show great potential as a low-cost solution for extracting lung pathology information.