Retrieval-Augmented Generation (RAG) has emerged as a powerful paradigm to enhance the factuality of Large Language Models (LLMs). However, existing RAG systems often suffer from an unfaithfulness issue, where the model's response contradicts evidence from the retrieved context. Existing approaches to improving contextual faithfulness largely rely on external interventions, such as prompt engineering, decoding constraints, or reward-based fine-tuning. These works treat the LLM as a black box and overlook a crucial question: how does the LLM internally integrate retrieved evidence with its parametric memory, particularly under knowledge conflicts? To address this gap, we conduct a probing-based analysis of hidden-state representations in LLMs and observe three findings: knowledge integration occurs hierarchically, conflicts manifest as latent signals at the sentence level, and irrelevant context is often amplified when aligned with parametric knowledge. Building on these findings, we propose CLEAR (Conflict-Localized and Enhanced Attention for RAG), a framework that (i) decomposes context into fine-grained sentence-level knowledge, (ii) employs hidden-state probing to localize conflicting knowledge, and (iii) introduces conflict-aware fine-tuning to guide the model to accurately integrate retrieved evidence. Extensive experiments across three benchmarks demonstrate that CLEAR substantially improves both accuracy and contextual faithfulness, consistently outperforming strong baselines under diverse conflict conditions. The related resources are available at https://github.com/LinfengGao/CLEAR.

Having been trained on massive pretraining data, large language models have shown excellent performance on many knowledge-intensive tasks. However, pretraining data tends to contain misleading and even conflicting information, and it is intriguing to understand how LLMs handle these noisy data during training. In this study, we systematically analyze LLMs' learning preferences for data with conflicting knowledge. We find that pretrained LLMs establish learning preferences similar to humans, i.e., preferences towards formal texts and texts with fewer spelling errors, resulting in faster learning and more favorable treatment of knowledge in data with such features when facing conflicts. This finding is generalizable across models and languages and is more evident in larger models. An in-depth analysis reveals that LLMs tend to trust data with features that signify consistency with the majority of data, and it is possible to instill new preferences and erase old ones by manipulating the degree of consistency with the majority data.

Providing knowledge documents for large language models (LLMs) has emerged as a promising solution to update the static knowledge inherent in their parameters. However, knowledge in the document may conflict with the memory of LLMs due to outdated or incorrect knowledge in the LLMs' parameters. This leads to the necessity of examining the capability of LLMs to assimilate supplemental external knowledge that conflicts with their memory. While previous studies have explained to what extent LLMs extract conflicting knowledge from the provided text, they neglect the necessity to reason with conflicting knowledge. Furthermore, there lack a detailed analysis on strategies to enable LLMs to resolve conflicting knowledge via prompting, decoding strategy, and supervised fine-tuning. To address these limitations, we construct a new dataset, dubbed KNOT, for knowledge conflict resolution examination in the form of question answering. KNOT facilitates in-depth analysis by dividing reasoning with conflicting knowledge into three levels: (1) Direct Extraction, which directly extracts conflicting knowledge to answer questions. (2) Explicit Reasoning, which reasons with conflicting knowledge when the reasoning path is explicitly provided in the question. (3) Implicit Reasoning, where reasoning with conflicting knowledge requires LLMs to infer the reasoning path independently to answer questions. We also conduct extensive experiments on KNOT to establish empirical guidelines for LLMs to utilize conflicting knowledge in complex circumstances. Dataset and associated codes can be accessed at https://github.com/THU-KEG/KNOT .

Prior work has uncovered a set of common problems in state-of-the-art context-based question answering (QA) systems: a lack of attention to the context when the latter conflicts with a model's parametric knowledge, little robustness to noise, and a lack of consistency with their answers. However, most prior work focus on one or two of those problems in isolation, which makes it difficult to see trends across them. We aim to close this gap, by first outlining a set of -- previously discussed as well as novel -- desiderata for QA models. We then survey relevant analysis and methods papers to provide an overview of the state of the field. The second part of our work presents experiments where we evaluate 15 QA systems on 5 datasets according to all desiderata at once. We find many novel trends, including (1) systems that are less susceptible to noise are not necessarily more consistent with their answers when given irrelevant context; (2) most systems that are more susceptible to noise are more likely to correctly answer according to a context that conflicts with their parametric knowledge; and (3) the combination of conflicting knowledge and noise can reduce system performance by up to 96%. As such, our desiderata help increase our understanding of how these models work and reveal potential avenues for improvements.