# Understanding the Impact of Confidence in Retrieval Augmented Generation: A Case Study in the Medical Domain

arXiv: https://arxiv.org/abs/2412.20309 · HTML: https://mlsanity.com/paper/2412.20309/

## Key facts

- Cited by 9 papers in the map (data through 14 Oct 2026).
- Placed in RAG pipeline design and evaluation, one of 15 directions in Retrieval-augmented generation.
- Builds on 26 of its 43 references that are in the map.
- First posted on arXiv 29 Dec 2024.

## Placed in

- Retrieval-augmented generation / [RAG pipeline design and evaluation](https://mlsanity.com/rag/rag-pipeline-design-and-evaluation/)

## Builds on (most cited first, 26 of 26)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [On Calibration of Modern Neural Networks](https://mlsanity.com/paper/1706.04599/) (2017)
- [Lost in the Middle: How Language Models Use Long Contexts](https://mlsanity.com/paper/2307.03172/) (2023)
- [Gemma 2: Improving Open Language Models at a Practical Size](https://mlsanity.com/paper/2408.00118/) (2024)
- [Phi-3 Technical Report: A Highly Capable Language Model Locally on Your Phone](https://mlsanity.com/paper/2404.14219/) (2024)
- [Self-RAG: Learning to Retrieve, Generate, and Critique through Self-Reflection](https://mlsanity.com/paper/2310.11511/) (2023)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Measuring Calibration in Deep Learning](https://mlsanity.com/paper/1904.01685/) (2019)
- [How Can We Know When Language Models Know? On the Calibration of Language Models for Question Answering](https://mlsanity.com/paper/2012.00955/) (2020)
- [Beyond temperature scaling: Obtaining well-calibrated multiclass probabilities with Dirichlet calibration](https://mlsanity.com/paper/1910.12656/) (2019)
- [Benchmarking Retrieval-Augmented Generation for Medicine](https://mlsanity.com/paper/2402.13178/) (2024)
- [Verified Uncertainty Calibration](https://mlsanity.com/paper/1909.10155/) (2019)
- [A Survey of Confidence Estimation and Calibration in Large Language Models](https://mlsanity.com/paper/2311.08298/) (2023)
- [LM-Polygraph: Uncertainty Estimation for Language Models](https://mlsanity.com/paper/2311.07383/) (2023)
- [SAC3: Reliable Hallucination Detection in Black-Box Language Models via Semantic-aware Cross-check Consistency](https://mlsanity.com/paper/2311.01740/) (2023)
- [Stop Measuring Calibration When Humans Disagree](https://mlsanity.com/paper/2210.16133/) (2022)
- [Improving Retrieval for RAG based Question Answering Models on Financial Documents](https://mlsanity.com/paper/2404.07221/) (2024)
- [Rationale-Guided Retrieval Augmented Generation for Medical Question Answering](https://mlsanity.com/paper/2411.00300/) (2024)
- [LLM-jp: A Cross-organizational Project for the Research and Development of Fully Open Japanese LLMs](https://mlsanity.com/paper/2407.03963/) (2024)
- [Cycles of Thought: Measuring LLM Confidence through Stable Explanations](https://mlsanity.com/paper/2406.03441/) (2024)
- [Exploring Predictive Uncertainty and Calibration in NLP: A Study on the Impact of Method & Data Scarcity](https://mlsanity.com/paper/2210.15452/) (2022)
- [Controlling Risk of Retrieval-augmented Generation: A Counterfactual Prompting Framework](https://mlsanity.com/paper/2409.16146/) (2024)
- [Can We Trust the Performance Evaluation of Uncertainty Estimation Methods in Text Summarization?](https://mlsanity.com/paper/2406.17274/) (2024)

## Built on by (most cited first, 9 of 9)

- [Retrieval-Augmented Generation: A Comprehensive Survey of Architectures, Enhancements, and Robustness Frontiers](https://mlsanity.com/paper/2506.00054/) (2025)
- [SearchRAG: Can Search Engines Be Helpful for LLM-based Medical Question Answering?](https://mlsanity.com/paper/2502.13233/) (2025)
- [NOVA: NOise-aware Verbal Confidence CAlibration for Robust Large Language Models in RAG Systems](https://mlsanity.com/paper/2601.11004/) (2026)
- [Transparentize the Internal and External Knowledge Utilization in LLMs with Trustworthy Citation](https://mlsanity.com/paper/2504.14856/) (2025)
- [IterKey: Iterative Keyword Generation with LLMs for Enhanced Retrieval Augmented Generation](https://mlsanity.com/paper/2505.08450/) (2025)
- [Decoding Uncertainty: The Impact of Decoding Strategies for Uncertainty Estimation in Large Language Models](https://mlsanity.com/paper/2509.16696/) (2025)
- [TextTIGER: Text-based Intelligent Generation with Entity Prompt Refinement for Text-to-Image Generation](https://mlsanity.com/paper/2504.18269/) (2025)
- [Identifying Influential N-grams in Confidence Calibration via Regression Analysis](https://mlsanity.com/paper/2604.05757/) (2026)
- [Less Data Approximates More: Earning Faithful Confidence in High-Stakes Domains](https://mlsanity.com/paper/2604.08454/) (2026)

## Abstract (arXiv)

Retrieval Augmented Generation (RAG) complements the knowledge of Large Language Models (LLMs) by leveraging external information to enhance response accuracy for queries. This approach is widely applied in several fields by taking its advantage of injecting the most up-to-date information, and researchers are focusing on understanding and improving this aspect to unlock the full potential of RAG in such high-stakes applications. However, despite the potential of RAG to address these needs, the mechanisms behind the confidence levels of its outputs remain underexplored. Our study focuses on the impact of RAG, specifically examining whether RAG improves the confidence of LLM outputs in the medical domain. We conduct this analysis across various configurations and models. We evaluate confidence by treating the model's predicted probability as its output and calculating several evaluation metrics which include calibration error method, entropy, the best probability, and accuracy. Experimental results across multiple datasets confirmed that certain models possess the capability to judge for themselves whether an inserted document relates to the correct answer. These results suggest that evaluating models based on their output probabilities determine whether they function as generators in the RAG framework. Our approach allows us to evaluate whether the models handle retrieved documents.