A Unified Mechanistic Analysis of Knowledge- and Safety-Based Refusals
Authors: Yuri Son, Seunghee Kim, Hyuhng Joon Kim, Taeuk Kim
Organizations: 1Hanyang University · 2Samsung Electronics
Abstract
Large language models (LLMs) are increasingly trained to decline queries that fall outside their knowledge (knowledge-based refusal, KR) or violate safety policies (safety-based refusal, SR). Although KR and SR result in superficially similar responses, they have largely been studied in isolation, leaving open whether they share an underlying mechanism. We address this gap with a systematic study on a new dataset of 213 contrastive quadruples that jointly probe both refusal types. We find that KR and SR are governed by overlapping yet distinguishable mechanisms. Both share a refusal direction, yet the overlap is asymmetric: SR signals transfer more strongly to KR than the reverse. Type-specific specialization emerges mainly in upper layers, with KR aligning with uncertainty- and knowledge-related representations and SR with safety- and policy-related ones. We thus characterize refusal as a commit-then-specify process: a shared initial mechanism commits to refusing, then type-specific features in later layers specify whether the grounds are epistemic or normative.
Large reasoning models (LRMs) generate chain-of-thought (CoT) traces before producing final outputs, introducing a dynamic internal state that may complicate control mechanisms such as refusal. Unlike instruction-tuned LLMs, where refusal is mediated by a single directional subspace, refusal in large reasoning models (LRMs) additionally depends on the CoT. In DeepSeek-R1-Distill-LLaMA-8B, activation steering reverses refusal in only 39% of cases when the CoT is kept fixed, but removing the CoT entirely increases this to 70%, indicating that the CoT actively reinforces refusal. In a two-stage intervention where the model regenerates its CoT under activation steering, refusal is reversed in 94% of cases, while the resulting CoT alone retains 48% of this effect even after steering is removed. This suggests that the CoT can carry and reconstruct the compliance signal independently. These findings indicate that refusal in LRMs is jointly encoded in residual stream activations and CoT. This joint activation makes LRM more robust against activation-level interventions alone, but exposes CoT to a possible alternative surface attack.
Safety-aligned large language models (LLMs) often generate refusal responses to harmless queries due to the over-refusal problem. However, existing methods for mitigating over-refusal cannot maintain a low refusal ratio for harmless queries while keeping a high refusal ratio for malicious ones. In this paper, we analyze how system prompts with varying safety levels affect LLM refusal behaviors when facing over-refusal queries. A key observation is that, when LLMs suffer from the over-refusal issue, non-refusal tokens remain present in the next-token candidate list, but the model systematically fails to select them, despite the generation of refusal tokens. Based on this observation, we propose a training-free and model-agnostic approach, Adaptive Contrastive Decoding (AdaCD), to mitigate over-refusal while maintaining LLM safety. First, AdaCD compares the output distributions of the LLM with or without an extreme safety system prompt to refine the refusal token distribution. Second, we introduce an adaptive contrastive decoding strategy that dynamically incorporates or removes the refusal token distribution, adaptively boosting the probability of selecting refusal or non-refusal tokens. Experimental results on five benchmark datasets show that, on average, AdaCD reduces the refusal ratio for over-refusal queries by 10.35%, yet still increases the refusal ratio for malicious queries by 0.13%. Code is available at https://github.com/OutdoorManofML/AdaCD.
Safety training on language models often induces over-refusal: improved safety on harmful prompts at the cost of increased refusal on harmless ones. Though this trade-off can be mitigated by training models with reinforcement learning (RL) to reason before answering, it does not remove the underlying problem that reasoning can often be a "rubber stamp" for a predetermined response. In this paper, we address the safety-refusal trade-off by rethinking how models are trained to reason about safety. Our key insight is that unsafe reasoning can itself serve as a useful exploratory signal. Rather than preemptively blocking harmful thoughts, we encourage the model to sufficiently explore unsafe reasoning but produce a safe response. The harmful exploration improves the model's ability to distinguish harmful from harmless prompts by resolving ambiguity, allowing it to remain safe while complying only when appropriate. We cast this as an adversarial optimization problem in which a reasoning player explores strategies for producing an unsafe response and an answer player ensures that the final output is safe. We train a single model with dense rewards to play both roles within one chain-of-thought, across different segments. To achieve this, we find that process rewards are crucial for stable optimization of competing objectives. Our resulting model SEAR deliberately engages in harmful reasoning as exploration while reliably flipping back to a safe answer. We demonstrate that this behavior helps mitigate over-refusal and defend against attacks that directly manipulate the reasoning to be harmful.