Safeguarding RAG Pipelines with GMTP: A Gradient-based Masked Token Probability Method for Poisoned Document Detection

Abstract: Retrieval-Augmented Generation (RAG) enhances LLMs by providing external knowledge for accurate and up-to-date responses. However, this reliance on external sources exposes a security risk, attackers can inject poisoned documents into the knowledge base to steer the generation process toward harmful or misleading outputs. In this paper, we propose Gradient-based Masked Token Probability (GMTP), a novel defense method to detect and filter out adversarially crafted documents. Specifically, GMTP identifies high-impact tokens by examining gradients of the retriever's similarity function. These key tokens are then masked, and their probabilities are checked via a Masked LLM (MLM). Since injected tokens typically exhibit markedly low masked-token probabilities, this enables GMTP to easily detect malicious documents and achieve high-precision filtering. Experiments demonstrate that GMTP is able to eliminate over 90% of poisoned content while retaining relevant documents, thus maintaining robust retrieval and generation performance across diverse datasets and adversarial settings.