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Clinical Context Variables Collectively Rival Model Choice in Embedding-Based Retrieval: Multi-Corpus Benchmark

Yngve Mikkelsen1

  • 1Saïd Business School, University of Oxford, Oxford, England, United Kingdom.

JMIR Medical Informatics
|May 7, 2026
PubMed
Summary

Clinical context variables significantly impact retrieval performance in retrieval-augmented generation (RAG) systems, comparable to embedding model choice. Local validation is crucial for clinical RAG deployment due to performance variations across corpora.

Keywords:
BM25benchmarkclinical documentationclinical informaticsdense retrievalembedding modelsretrieval-augmented generation

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Area of Science:

  • Medical Informatics
  • Natural Language Processing
  • Artificial Intelligence in Healthcare

Background:

  • Retrieval-augmented generation (RAG) systems enhance clinical decision-making by integrating evidence from large language models.
  • Effective retrieval is critical for RAG, as downstream generation cannot compensate for missed documents.
  • Current embedding model selection for clinical RAG often relies on general-domain benchmarks, which may not generalize to diverse clinical data.

Purpose of the Study:

  • To evaluate the impact of clinical context variables (corpus type, query format) on retrieval performance in RAG.
  • To compare the influence of context variables against embedding model choice for clinical retrieval tasks.
  • To determine the generalizability of general-domain embedding model rankings to clinical retrieval.

Main Methods:

  • Benchmarked 13 retrieval configurations, including 10 embedding models and a BM25 baseline, across three clinical corpora (MTSamples, PMC-Patients, synthetic notes).
  • Evaluated 12 embedding configurations across 3 corpora, 2 query formats (keyword vs. natural language), and 4 chunking strategies (294 conditions total).
  • Utilized factorial ANOVA with η² effect sizes to quantify relative contributions of factors and interactions on retrieval metrics like MRR@10.

Main Results:

  • Embedding model choice accounted for 40.8% of variance in MRR@10, while corpus type (24.6%) and query format (19.2%) also significantly contributed.
  • Combined context variables (corpus, query format, interactions) explained 49.0% of variance, nearly matching model-related effects (47.6%).
  • Model rankings shifted across corpora, indicating poor portability; domain-specific models underperformed general-purpose embeddings.

Conclusions:

  • Clinical context variables significantly influence retrieval performance, rivaling embedding model choice.
  • Embedding model rankings are not universally portable across different clinical documentation types.
  • Mandatory local validation of RAG systems is essential, rather than relying on general-domain benchmarks.