Retrieval-augmented generation (RAG) systems enhance large language models (LLMs) with external knowledge but are vulnerable to corpus poisoning and contamination attacks, which can compromise output integrity. Existing defenses often apply aggressive filtering, leading to unnecessary loss of valuable information and reduced reliability in generation. To address this problem, we propose a two-stage semantic filtering and conflict-free framework for trustworthy RAG. In the first stage, we perform a joint filter with semantic and cluster-based filtering which is guided by the Entity-intent-relation extractor (EIRE). EIRE extracts entities, latent objectives, and entity relations from both the user query and filtered documents, scores their semantic relevance, and selectively adds valuable documents into the clean retrieval database. In the second stage, we proposed an EIRE-guided conflict-aware filtering module, which analyzes semantic consistency between the query, candidate answers, and retrieved knowledge before final answer generation, filtering out internal and external contradictions that could mislead the model. Through this two-stage process, SeCon-RAG effectively preserves useful knowledge while mitigating conflict contamination, achieving significant improvements in both generation robustness and output trustworthiness. Extensive experiments across various LLMs and datasets demonstrate that the proposed SeCon-RAG markedly outperforms state-of-the-art defense methods.

In recent years, data poisoning attacks have been increasingly designed to appear harmless and even beneficial, often with the intention of verifying dataset ownership or safeguarding private data from unauthorized use. However, these developments have the potential to cause misunderstandings and conflicts, as data poisoning has traditionally been regarded as a security threat to machine learning systems. To address this issue, it is imperative for harmless poisoning generators to claim ownership of their generated datasets, enabling users to identify potential poisoning to prevent misuse. In this paper, we propose the deployment of watermarking schemes as a solution to this challenge. We introduce two provable and practical watermarking approaches for data poisoning: {\em post-poisoning watermarking} and {\em poisoning-concurrent watermarking}. Our analyses demonstrate that when the watermarking length is $Θ(\sqrt{d}/ε_w)$ for post-poisoning watermarking, and falls within the range of $Θ(1/ε_w^2)$ to $O(\sqrt{d}/ε_p)$ for poisoning-concurrent watermarking, the watermarked poisoning dataset provably ensures both watermarking detectability and poisoning utility, certifying the practicality of watermarking under data poisoning attacks. We validate our theoretical findings through experiments on several attacks, models, and datasets.