# VaccineRAG: Boosting Multimodal Large Language Models' Immunity to Harmful RAG Samples

arXiv: https://arxiv.org/abs/2509.04502 · HTML: https://mlsanity.com/paper/2509.04502/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Document understanding and multimodal RAG, one of 16 directions in Multimodal LLMs / vision-language models.
- Builds on 21 of its 28 references that are in the map.
- First posted on arXiv 2 Sep 2025.

## Placed in

- Multimodal LLMs / vision-language models / [Document understanding and multimodal RAG](https://mlsanity.com/mllm/document-understanding-and-multimodal-rag/)
- Retrieval-augmented generation / [RAG robustness and adaptive retrieval](https://mlsanity.com/rag/rag-robustness-and-adaptive-retrieval/)

## Builds on (most cited first, 21 of 21)

- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Parameter-Efficient Transfer Learning for NLP](https://mlsanity.com/paper/1902.00751/) (2019)
- [Qwen2-VL: Enhancing Vision-Language Model's Perception of the World at Any Resolution](https://mlsanity.com/paper/2409.12191/) (2024)
- [Prefix-Tuning: Optimizing Continuous Prompts for Generation](https://mlsanity.com/paper/2101.00190/) (2021)
- [InternVL: Scaling up Vision Foundation Models and Aligning for Generic Visual-Linguistic Tasks](https://mlsanity.com/paper/2312.14238/) (2023)
- [Retrieval-Augmented Generation for Large Language Models: A Survey](https://mlsanity.com/paper/2312.10997/) (2023)
- [Learn to Explain: Multimodal Reasoning via Thought Chains for Science Question Answering](https://mlsanity.com/paper/2209.09513/) (2022)
- [M3-Embedding: Multi-Linguality, Multi-Functionality, Multi-Granularity Text Embeddings Through Self-Knowledge Distillation](https://mlsanity.com/paper/2402.03216/) (2024)
- [Multimodal Chain-of-Thought Reasoning in Language Models](https://mlsanity.com/paper/2302.00923/) (2023)
- [In-Context Retrieval-Augmented Language Models](https://mlsanity.com/paper/2302.00083/) (2023)
- [Compacter: Efficient Low-Rank Hypercomplex Adapter Layers](https://mlsanity.com/paper/2106.04647/) (2021)
- [LLaVA-CoT: Let Vision Language Models Reason Step-by-Step](https://mlsanity.com/paper/2411.10440/) (2024)
- [LongRAG: Enhancing Retrieval-Augmented Generation with Long-context LLMs](https://mlsanity.com/paper/2406.15319/) (2024)
- [MegaPairs: Massive Data Synthesis For Universal Multimodal Retrieval](https://mlsanity.com/paper/2412.14475/) (2024)
- [Wiki-LLaVA: Hierarchical Retrieval-Augmented Generation for Multimodal LLMs](https://mlsanity.com/paper/2404.15406/) (2024)
- [Towards Better Chain-of-Thought Prompting Strategies: A Survey](https://mlsanity.com/paper/2310.04959/) (2023)
- [EchoSight: Advancing Visual-Language Models with Wiki Knowledge](https://mlsanity.com/paper/2407.12735/) (2024)
- [MLLM Is a Strong Reranker: Advancing Multimodal Retrieval-augmented Generation via Knowledge-enhanced Reranking and Noise-injected Training](https://mlsanity.com/paper/2407.21439/) (2024)
- [UniFashion: A Unified Vision-Language Model for Multimodal Fashion Retrieval and Generation](https://mlsanity.com/paper/2408.11305/) (2024)
- [Towards Retrieval-Augmented Architectures for Image Captioning](https://mlsanity.com/paper/2405.13127/) (2024)

## Abstract (arXiv)

Retrieval Augmented Generation enhances the response accuracy of Large Language Models (LLMs) by integrating retrieval and generation modules with external knowledge, demonstrating particular strength in real-time queries and Visual Question Answering tasks. However, the effectiveness of RAG is frequently hindered by the precision of the retriever: many retrieved samples fed into the generation phase are irrelevant or misleading, posing a critical bottleneck to LLMs' performance. To address this challenge, we introduce VaccineRAG, a novel Chain-of-Thought-based retrieval-augmented generation dataset. On one hand, VaccineRAG employs a benchmark to evaluate models using data with varying positive/negative sample ratios, systematically exposing inherent weaknesses in current LLMs. On the other hand, it enhances models' sample-discrimination capabilities by prompting LLMs to generate explicit Chain-of-Thought (CoT) analysis for each sample before producing final answers. Furthermore, to enhance the model's ability to learn long-sequence complex CoT content, we propose Partial-GRPO. By modeling the outputs of LLMs as multiple components rather than a single whole, our model can make more informed preference selections for complex sequences, thereby enhancing its capacity to learn complex CoT. Comprehensive evaluations and ablation studies on VaccineRAG validate the effectiveness of the proposed scheme. The code and dataset will be publicly released soon.