# Health System Scale Semantic Search Across Unstructured Clinical Notes

arXiv: https://arxiv.org/abs/2604.25605 · HTML: https://mlsanity.com/paper/2604.25605/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 30 references that are in the map.
- First posted on arXiv 28 Apr 2026.

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

- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Qwen3 Embedding: Advancing Text Embedding and Reranking Through Foundation Models](https://mlsanity.com/paper/2506.05176/) (2025)
- [Text Embeddings by Weakly-Supervised Contrastive Pre-training](https://mlsanity.com/paper/2212.03533/) (2022)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Nomic Embed: Training a Reproducible Long Context Text Embedder](https://mlsanity.com/paper/2402.01613/) (2024)
- [MMTEB: Massive Multilingual Text Embedding Benchmark](https://mlsanity.com/paper/2502.13595/) (2025)
- [Pooling And Attention: What Are Effective Designs For LLM-Based Embedding Models?](https://mlsanity.com/paper/2409.02727/) (2024)
- [PubMed and Beyond: Biomedical Literature Search in the Age of Artificial Intelligence](https://mlsanity.com/paper/2307.09683/) (2023)

## Abstract (arXiv)

Introduction: Semantic search, which retrieves documents based on conceptual similarity rather than keywords, offers advantages for retrieval of clinical information. However, deploying semantic search across health systems, comprising hundreds of millions of clinical notes, presents formidable engineering, cost, and governance challenges that have prevented institutional adoption. Methods: We deployed a semantic search system at a large children's hospital indexing 166 million clinical notes (484 million embedding vectors) from 1.68 million patients. The system uses instruction-tuned qwen3-embedding-0.6B embeddings, stores vectors with storage-optimized indexing, maintains full-text metadata in a low-latency key-value store, and operates within a HIPAA-compliant governance framework. We evaluated the system by optimizing the model and chunking strategy using a physician-authored benchmark, characterizing full-scale performance (cost, latency, retrieval quality), and assessing clinical utility via chart abstraction efficiency and comparison to ICD-10 cohort generation. Results: The system delivers sub-second query latency with monthly operational costs of ~USD 4,000. Qwen3 embeddings with 300-token chunk size achieved 94.6% accuracy on the benchmark. In clinical utility evaluation across three abstraction tasks, semantic search reduced time-to-completion by 24 to 89% versus chart review while maintaining inter-rater agreement where assessable. During system-wide retrieval, semantic search recovered 98% of patients with molecularly confirmed genetic diseases, versus at most 75% by diagnosis codes. Conclusion: Health-system-scale semantic search is technically and operationally feasible. The system provides institutional infrastructure supporting interactive search, cohort generation, and downstream LLM-powered clinical applications without requiring specialized informatics expertise.