Evaluating Factual Density in Multi-Source RAG: A Study in Medical AI Accuracy

Retrieval-Augmented Generation (RAG) offers a well-established path to grounding large language model (LLM) outputs in external knowledge, yet the question of which retrieval strategy works best in a high-stakes domain such as biomedicine has not received the controlled, multi-metric treatment it deserves. This paper presents a systematic empirical comparison of five retrieval strategies -- Dense Vector Search, Hybrid BM25 + Dense retrieval, Cross-Encoder Reranking, Multi-Query Expansion, and Maximal Marginal Relevance (MMR) -- within a biomedical question-answering RAG pipeline. All strategies share a fixed generation model (GPT-4o-mini), a common vector store (ChromaDB), and OpenAI's text-embedding-3-small embeddings, ensuring that observed differences are attributable to retrieval alone. Evaluation is conducted on 250 question-answer pairs drawn from a preprocessed subset of the BioASQ benchmark (rag-mini-bioasq) using four DeepEval metrics: contextual precision, contextual recall, faithfulness, and answer relevancy, each reported with 95% confidence intervals. A no-context ablation is included as a lower bound. Cross-Encoder Reranking achieves the best composite score (0.827) and highest contextual precision (0.852), confirming that query-document interaction yields measurable retrieval gains. Multi-Query Expansion, despite its recall-oriented design, produces the weakest contextual precision (0.671), suggesting naive query diversification introduces retrieval noise. MMR sacrifices answer relevancy for diversity, while the Dense baseline (composite 0.822) falls within 0.005 points of the top strategy. All RAG conditions dramatically outperform the no-context ablation on answer relevancy (0.658-0.701 vs. 0.287), confirming the practical value of retrieval. The full pipeline, hyperparameters, and evaluation code are publicly available.

Medical question answering is a high-stakes setting where factual errors can have serious consequences. Retrieval-augmented generation (RAG) is widely viewed as a promising solution, and prior work has reported substantial gains for large medical QA models. We revisit this assumption across a broad range of open-weight instruction-tuned models spanning 7B to 72B parameters. Across five models, ten biomedical QA datasets, four retrieval methods, and four retrieval corpora, we find that retrieval yields only small and inconsistent improvements over a no-retrieval baseline, typically within 1-2 points. In contrast, the choice of backbone model has a much larger effect than the choice of retriever or corpus, and expert and layman retrieval sources perform similarly in most settings. These results suggest that the main bottleneck is not retrieval quality alone, but the model's limited ability to use retrieved evidence effectively.

Incorporating specific knowledge into large language models via retrieval-augmented generation (RAG) is a widespread technique that fuels many of today's industry AI applications. A fundamental problem is to assess if the context retrieved by some similarity search provides indeed supporting facts, or instead misguides the generator with irrelevant information. It is critical to associate meaningful confidence measures about the factuality of the retrieval process with the generated answers. We present a new, two-staged approach to predict fact faithfulness of the output of retrieval-augmented generations. First, we employ conformal prediction to select only those retrieved chunks who have a high chance to come from the correct source. This approach in itself can improve answer quality by up to 6% in some of the studied datasets, however, the associated statistical guarantees do not hold generally, since the assumption of sample exchangeability depends on the retriever setup. We present diagnostic metrics to assess whether a setup is suitable. Second, we quantify confidence in the consistency of a generated final answer with a given retrieved context, using an attention-based factuality classifier. This approach can detect inconsistent answers with a chance of up to 77%. Our work helps to establish a novel type of certified RAG systems for a broad range of natural language industry applications.