# SeCon-RAG: A Two-Stage Semantic Filtering and Conflict-Free Framework for Trustworthy RAG

arXiv: https://arxiv.org/abs/2510.09710 · HTML: https://mlsanity.com/paper/2510.09710/

## Key facts

- Cited by 13 papers in the map (data through 14 Oct 2026).
- Placed in RAG robustness and adaptive retrieval, one of 15 directions in Retrieval-augmented generation.
- Builds on 41 of its 55 references that are in the map.
- First posted on arXiv 10 Oct 2025.

## Placed in

- Retrieval-augmented generation / [RAG robustness and adaptive retrieval](https://mlsanity.com/rag/rag-robustness-and-adaptive-retrieval/)

## Builds on (most cited first, 30 of 41)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [HotpotQA: A Dataset for Diverse, Explainable Multi-hop Question Answering](https://mlsanity.com/paper/1809.09600/) (2018)
- [Qwen Technical Report](https://mlsanity.com/paper/2309.16609/) (2023)
- [A Survey of Large Language Models](https://mlsanity.com/paper/2303.18223/) (2023)
- [SimCSE: Simple Contrastive Learning of Sentence Embeddings](https://mlsanity.com/paper/2104.08821/) (2021)
- [MS MARCO: A Human Generated MAchine Reading COmprehension Dataset](https://mlsanity.com/paper/1611.09268/) (2016)
- [MiniLM: Deep Self-Attention Distillation for Task-Agnostic Compression of Pre-Trained Transformers](https://mlsanity.com/paper/2002.10957/) (2020)
- [Not what you've signed up for: Compromising Real-World LLM-Integrated Applications with Indirect Prompt Injection](https://mlsanity.com/paper/2302.12173/) (2023)
- [Qwen2.5-Coder Technical Report](https://mlsanity.com/paper/2409.12186/) (2024)
- [M3-Embedding: Multi-Linguality, Multi-Functionality, Multi-Granularity Text Embeddings Through Self-Knowledge Distillation](https://mlsanity.com/paper/2402.03216/) (2024)
- [AgentPoison: Red-teaming LLM Agents via Poisoning Memory or Knowledge Bases](https://mlsanity.com/paper/2407.12784/) (2024)
- [PoisonedRAG: Knowledge Corruption Attacks to Retrieval-Augmented Generation of Large Language Models](https://mlsanity.com/paper/2402.07867/) (2024)
- [Query Rewriting for Retrieval-Augmented Large Language Models](https://mlsanity.com/paper/2305.14283/) (2023)
- [Take a Step Back: Evoking Reasoning via Abstraction in Large Language Models](https://mlsanity.com/paper/2310.06117/) (2023)
- [Poisoning Retrieval Corpora by Injecting Adversarial Passages](https://mlsanity.com/paper/2310.19156/) (2023)
- [Certifiably Robust RAG against Retrieval Corruption](https://mlsanity.com/paper/2405.15556/) (2024)
- [Improved Techniques for Optimization-Based Jailbreaking on Large Language Models](https://mlsanity.com/paper/2405.21018/) (2024)
- [Machine Against the RAG: Jamming Retrieval-Augmented Generation with Blocker Documents](https://mlsanity.com/paper/2406.05870/) (2024)
- [BadRAG: Identifying Vulnerabilities in Retrieval Augmented Generation of Large Language Models](https://mlsanity.com/paper/2406.00083/) (2024)
- [Retrieval-Augmented Generation for Natural Language Processing: A Survey](https://mlsanity.com/paper/2407.13193/) (2024)
- [SuRe: Summarizing Retrievals using Answer Candidates for Open-domain QA of LLMs](https://mlsanity.com/paper/2404.13081/) (2024)
- [TrojanRAG: Retrieval-Augmented Generation Can Be Backdoor Driver in Large Language Models](https://mlsanity.com/paper/2405.13401/) (2024)
- [Astute RAG: Overcoming Imperfect Retrieval Augmentation and Knowledge Conflicts for Large Language Models](https://mlsanity.com/paper/2410.07176/) (2024)
- [Practical Poisoning Attacks against Retrieval-Augmented Generation](https://mlsanity.com/paper/2504.03957/) (2025)
- [Poison-RAG: Adversarial Data Poisoning Attacks on Retrieval-Augmented Generation in Recommender Systems](https://mlsanity.com/paper/2501.11759/) (2025)
- [PR-Attack: Coordinated Prompt-RAG Attacks on Retrieval-Augmented Generation in Large Language Models via Bilevel Optimization](https://mlsanity.com/paper/2504.07717/) (2025)

## Built on by (most cited first, 13 of 13)

- [A Survey on Long-Term Memory Security in LLM Agents: Attacks, Defenses, and Governance Across the Memory Lifecycle](https://mlsanity.com/paper/2604.16548/) (2026)
- [Seeing Is Not Screening: Multimodal Hidden Instruction Attacks on Agent Skill Scanners](https://mlsanity.com/paper/2606.18198/) (2026)
- [Addressing Corpus Knowledge Poisoning Attacks on RAG Using Sparse Attention](https://mlsanity.com/paper/2602.04711/) (2026)
- [Securing Retrieval-Augmented Generation: A Taxonomy of Attacks, Defenses, and Future Directions](https://mlsanity.com/paper/2604.08304/) (2026)
- [Retrieval Pivot Attacks in Hybrid RAG: Measuring and Mitigating Amplified Leakage from Vector Seeds to Graph Expansion](https://mlsanity.com/paper/2602.08668/) (2026)
- [Needle-in-RAG: Prompt-Conditioned Character-Level Traceback of Poisoned Spans in Retrieved Evidence](https://mlsanity.com/paper/2605.01782/) (2026)
- [Retrieved But Not Reliable: A Survey on Attacks, and Defenses in Retrieval-Augmented Generation](https://mlsanity.com/paper/2608.24977/) (2026)
- [BiRD: A Bidirectional Ranking Defense Mechanism for Retrieval Augmented Generation](https://mlsanity.com/paper/2605.20123/) (2026)
- [When Poison Fails After Retrieval: Revisiting Corpus Poisoning under Chunking and Reranking Pipelines](https://mlsanity.com/paper/2606.11265/) (2026)
- [Tracing Target Answers in Poisoned Retrieval Corpora via Token Influence Attribution](https://mlsanity.com/paper/2606.25721/) (2026)
- [RAGSieve: Self-Referenced Local Contrast for Knowledge-Poison Detection in Retrieval-Augmented Generation](https://mlsanity.com/paper/2608.13010/) (2026)
- [Divide and Doubt: Diverse Distributed Poisoning for Retrieval-Augmented Generation](https://mlsanity.com/paper/2609.27090/) (2026)
- [RAG-PIBench: A Leakage-Aware Benchmark for Prompt-Injection Detection in Trustworthy RAG Systems](https://mlsanity.com/paper/2610.08571/) (2026)

## Abstract (arXiv)

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.