# Domain Fine-Tuning vs. Retrieval-Augmented Generation for Medical Multiple-Choice Question Answering: A Controlled Comparison at the 4B-Parameter Scale

arXiv: https://arxiv.org/abs/2604.23801 · HTML: https://mlsanity.com/paper/2604.23801/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical and biomedical RAG, one of 15 directions in Retrieval-augmented generation.
- Builds on 10 of its 13 references that are in the map.
- First posted on arXiv 26 Apr 2026.

## Placed in

- Retrieval-augmented generation / [Medical and biomedical RAG](https://mlsanity.com/rag/medical-and-biomedical-rag/)

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

- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [Gemma: Open Models Based on Gemini Research and Technology](https://mlsanity.com/paper/2403.08295/) (2024)
- [Capabilities of GPT-4 on Medical Challenge Problems](https://mlsanity.com/paper/2303.13375/) (2023)
- [MedMCQA : A Large-scale Multi-Subject Multi-Choice Dataset for Medical domain Question Answering](https://mlsanity.com/paper/2203.14371/) (2022)
- [MedGemma Technical Report](https://mlsanity.com/paper/2507.05201/) (2025)
- [Benchmarking Retrieval-Augmented Generation for Medicine](https://mlsanity.com/paper/2402.13178/) (2024)
- [Nomic Embed: Training a Reproducible Long Context Text Embedder](https://mlsanity.com/paper/2402.01613/) (2024)
- [Augmenting Black-box LLMs with Medical Textbooks for Biomedical Question Answering](https://mlsanity.com/paper/2309.02233/) (2023)

## Abstract (arXiv)

Practitioners deploying small open-weight large language models (LLMs) for medical question answering face a recurring design choice: invest in a domain-fine-tuned model, or keep a general-purpose model and inject domain knowledge at inference time via retrieval-augmented generation (RAG). We isolate this trade-off by holding model size, prompt template, decoding temperature, retrieval pipeline, and evaluation protocol fixed, and varying only (i) whether the model has been domain-adapted (Gemma 3 4B vs. MedGemma 4B, both 4-bit quantized and served via Ollama) and (ii) whether retrieved passages from a medical knowledge corpus are inserted into the prompt. We evaluate all four cells of this 2x2 design on the full MedQA-USMLE 4-option test split (1,273 questions) with three repetitions per question (15,276 LLM calls). Domain fine-tuning yields a +6.8 percentage-point gain in majority-vote accuracy over the general 4B baseline (53.3% vs. 46.4%, McNemar p < 10^-4). RAG over MedMCQA explanations does not produce a statistically significant gain in either model, and in the domain-tuned model the point estimate is slightly negative (-1.9 pp, p = 0.16). At this scale and on this benchmark, domain knowledge encoded in weights dominates domain knowledge supplied in context. We release the full experiment code and JSONL traces to support replication.