A Comparison of Independent and Joint Fine-tuning Strategies for Retrieval-Augmented Generation

Abstract: A Comparison of Independent and Joint Fine-tuning Strategies for Retrieval-Augmented Generation Download PDF Neal Gregory Lawton, Alfy Samuel, Anoop Kumar, Daben Liu Published: 20 Aug 2025, Last Modified: 17 Sept 2025EMNLP 2025 FindingsConference, Publication Chairs, AuthorsRevisionsBibTeXCC BY 4.0 Keywords: Retrieval-Augmented Generation (RAG), LLMs, Fine-tuning, Question Answering, Joint fine-tuning TL;DR: We evaluate and compare strategies for fine-tuning Retrieval Augmented Generation (RAG) pipelines, including independent fine-tuning, joint fine-tuning, and two-phase fine-tuning. Abstract: Retrieval augmented generation (RAG) is a popular framework for question answering that is powered by two LLMs: an embedding model that retrieves context documents from a database that are relevant to a given question, and a generator model that uses the retrieved context to generate an answer to the question. Both the embedding and generator models can be fine-tuned to increase performance of a RAG pipeline on a new task, but multiple fine-tuning strategies exist with different costs and benefits. In this paper, we evaluate and compare several RAG fine-tuning strategies, including independent, joint, and two-phase fine-tuning. In our experiments, we observe that all of these strategies achieve about equal improvement in EM and F1 generation quality metrics, although they have significantly different computational costs. We conclude the optimal fine-tuning strategy to use depends on whether the training dataset includes context labels and whether a grid search over the learning rates for the embedding and generator models is required.