Papers › Efficient and Reproducible Biomedical Question Answering using Retrieval Augmented Generation

Efficient and Reproducible Biomedical Question Answering using Retrieval Augmented Generation

12 May 2025arXiv:2505.07917archive 2025-07-28

Linus Stuhlmann, Michael Alexander Saxer, Jonathan Fürst

Biomedical question-answering (QA) systems require effective retrieval and generation components to ensure accuracy, efficiency, and scalability. This study systematically examines a Retrieval-Augmented Generation (RAG) system for biomedical QA, evaluating retrieval strategies and response time trade-offs. We first assess state-of-the-art retrieval methods, including BM25, BioBERT, MedCPT, and a hybrid approach, alongside common data stores such as Elasticsearch, MongoDB, and FAISS, on a ~10% subset of PubMed (2.4M documents) to measure indexing efficiency, retrieval latency, and retriever performance in the end-to-end RAG system. Based on these insights, we deploy the final RAG system on the full 24M PubMed corpus, comparing different retrievers' impact on overall performance. Evaluations of the retrieval depth show that retrieving 50 documents with BM25 before reranking with MedCPT optimally balances accuracy (0.90), recall (0.90), and response time (1.91s). BM25 retrieval time remains stable (82ms), while MedCPT incurs the main computational cost. These results highlight previously not well-known trade-offs in retrieval depth, efficiency, and scalability for biomedical QA. With open-source code, the system is fully reproducible and extensible.

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Question Answering RAG Reranking Retrieval Retrieval-augmented Generation

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Adam Attention Attention Dropout BART BERT BPE Dense Connections Dropout Layer Normalization Linear Layer Linear Warmup With Linear Decay Multi-Head Attention RAG Residual Connection Softmax Weight Decay WordPiece

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