# Configurable Clinical Information Extraction with Agentic RAG: What Works, What Breaks, and Why

arXiv: https://arxiv.org/abs/2606.19602 · HTML: https://mlsanity.com/paper/2606.19602/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Medical and biomedical RAG, one of 15 directions in Retrieval-augmented generation.
- Builds on 13 of its 38 references that are in the map.
- First posted on arXiv 17 Jun 2026.

## Placed in

- Retrieval-augmented generation / [Medical and biomedical RAG](https://mlsanity.com/rag/medical-and-biomedical-rag/)
- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 13 of 13)

- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Large Language Models are Few-Shot Clinical Information Extractors](https://mlsanity.com/paper/2205.12689/) (2022)
- [Let Me Speak Freely? A Study on the Impact of Format Restrictions on Performance of Large Language Models](https://mlsanity.com/paper/2408.02442/) (2024)
- [Multi-domain Clinical Natural Language Processing with MedCAT: the Medical Concept Annotation Toolkit](https://mlsanity.com/paper/2010.01165/) (2020)
- [PaddleOCR-VL-1.5: Towards a Multi-Task 0.9B VLM for Robust In-the-Wild Document Parsing](https://mlsanity.com/paper/2601.21957/) (2026)
- [Improving Retrieval-Augmented Generation in Medicine with Iterative Follow-up Questions](https://mlsanity.com/paper/2408.00727/) (2024)
- [ReflecTool: Towards Reflection-Aware Tool-Augmented Clinical Agents](https://mlsanity.com/paper/2410.17657/) (2024)
- [Collapse of Dense Retrievers: Short, Early, and Literal Biases Outranking Factual Evidence](https://mlsanity.com/paper/2503.05037/) (2025)
- [HARMON-E: Hierarchical Agentic Reasoning for Multimodal Oncology Notes to Extract Structured Data](https://mlsanity.com/paper/2512.19864/) (2025)
- [Serialisation Strategy Matters: How FHIR Data Format Affects LLM Medication Reconciliation](https://mlsanity.com/paper/2604.21076/) (2026)

## Built on by (most cited first, 1 of 1)

- [A Living Benchmark for Information Retrieval from Electronic Health Records](https://mlsanity.com/paper/2609.30205/) (2026)

## Abstract (arXiv)

Patient contexts span hundreds of heterogeneous documents and thousands of structured data points, yet the document-level metadata that AI systems need for retrieval and triage is absent or incomplete. Standard retrieval-augmented generation fails on this data, mishandling temporal reasoning, cross-document dependencies, and missing metadata. We deploy ACIE (Agentic Clinical Information Extraction) at University Medicine Essen: an on-premise agentic RAG pipeline that reasons over complete patient contexts and grounds every answer in source passages for clinician verification. We quantify the metadata gap, trace the architectural decisions it shaped, and evaluate extraction alongside an independent retrospective lymphoma registry study, in which nuclear-medicine physicians verify every extracted value against its cited sources. Across 7,326 judgments, clinicians accepted 96.5% of extractions, with per-type acceptance ranging from 80% to 99%.