# RAG-BioQA: A Retrieval-Augmented Generation Framework for Long-Form Biomedical Question Answering Source: [RAG-BioQA: A Retrieval-Augmented Generation Framework for Long-Form Biomedical Question Answering]() Collection index: [llms.txt]() Data updated: 2026-01-06T05:00:04.578Z Authors: Lovely Yeswanth Panchumarthi, Sumalatha Saleti, Sai Prasad Gudari, Atharva Negi, Praveen Raj Budime, Harsit Upadhya Published: 2025-10-02T02:49:09.000Z ## Abstract The rapidly growth of biomedical literature creates challenges acquiring specific medical information. Current biomedical question-answering systems primarily focus on short-form answers, failing to provide comprehensive explanations necessary for clinical decision-making. We present RAG-BioQA, a retrieval-augmented generation framework for long-form biomedical question answering. Our system integrates BioBERT embeddings with FAISS indexing for retrieval and a LoRA fine-tuned FLAN-T5 model for answer generation. We train on 181k QA pairs from PubMedQA, MedDialog, and MedQuAD, and evaluate on a held-out PubMedQA test set. We compare four retrieval strategies: dense retrieval (FAISS), BM25, ColBERT, and MonoT5. Our results show that domain-adapted dense retrieval outperforms zero-shot neural re-rankers, with the best configuration achieving 0.24 BLEU-1 and 0.29 ROUGE-1. Fine-tuning improves BERTScore by 81\\% over the base model. We release our framework to support reproducible biomedical QA research. ## Recorded benchmark results A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage. ## Original sources and implementation [Original paper]() [PDF]()