Retrieval-Augmented Generation (RAG) systems often fail to maintain contextual faithfulness, generating responses that conflict with the provided context. Existing methods attempt to improve faithfulness through external interventions, such as specialized prompting, decoding-based calibration, or preference optimization. However, since these approaches treat the LLM as a black box, they lack a reliable mechanism to assess how these conflicts occur. Consequently, they tend to be brittle, data-intensive, and agnostic to the model’s internal reasoning process. In this paper, we move beyond black-box interventions to analyze the model’s internal reasoning process. We discover that conflicting and aligned knowledge states are linearly separable in the model’s latent space, and contextual noise systematically increases the entropy of these representations. Based on these findings, we propose ProbeRAG, a novel framework for faithful RAG that operates in three stages: (i) fine-grained knowledge pruning to filter irrelevant context, (ii) latent conflict probing to identify hard conflicts in the model’s latent space, and (iii) conflict-aware attention to modulate attention heads toward faithful context integration. Extensive experiments demonstrate that ProbeRAG substantially improves both accuracy and contextual faithfulness. The related resources are available at https://github.com/XMUDeepLIT/ProbeRAG.

Retrieval-Augmented Generation (RAG) has long been a promising paradigm for enhancing large language models (LLMs) with external knowledge. Traditional embedding-based methods for graph construction can capture semantic similarity but struggle to establish fine-grained, interpretable logical relationships. Recently, Graph-enhanced RAG (GraphRAG) has gained increasing popularity for its capability in modeling logical relationships. However, graph construction requires extensive token consumption for triple extraction and summarization, making it costly and slow. Accordingly, we propose MeshRAG, a novel framework for mining efficient structures via hashing to enhance RAG. We adopt an inductive paradigm in which global graph structure emerges from local hash collisions rather than explicit symbolic extraction. By replacing neural embedding search with lightweight and bitwise operations, MeshRAG automates a simple and rapid graph construction process. Furthermore, the hash collision mechanism provides transparent evidence for logical connections and retrieval decisions. Experimental results show that MeshRAG outperforms existing baselines, while its graph construction requires no GPU resources or token budget and can structure over ten thousand chunks in a few minutes.