How do the methods used to train language models to refuse harmful requests shape how that refusal actually works inside the model? We compare three post-training methods - supervised fine-tuning, reasoning-augmented fine-tuning (training on reasoning chains that justify a safety decision), and preference optimization (ORPO) - across three architecturally distinct models (Llama-3.1-8B, Gemma-2-9B, Qwen3-8B). We find that training method, not just data, reshapes how refusal is computed internally: reasoning-augmented training consistently produces a distinct kind of refusal computation, visible across all three models, while architecture independently shapes internal structure and how reliably refusal can be steered. Most importantly, no method we study achieves all three properties we would want from safe alignment at once: refusal that isn't concentrated in a few fragile components, safety gains that don't cost general capability, and safety behavior correctable through small, targeted edits. We caution against treating current post-training methods as a solved, reliable defense, especially for security-critical use. Code and models are available in https://github.com/hoangcuongnguyen2001/Beyond-Shallow-Alignment.
Large language models typically undergo post-training to align them with safety policies but there exist many sophisticated jailbreaks that sidestep established safeguards. For instance, prior work by Andriushchenko et al. (2025) has found that changing the grammatical tense from present to past can be enough to elicit harmful responses. In this work, we uncover a more general failure of non-imperative syntactic forms. We demonstrate that this syntactic vulnerability exists in 16 models up to 70B parameters, using behavioral evaluation. To investigate the root cause, we apply causal mediation analysis, finding that refusal is partially conditioned on upstream syntactic features. By steering these purely syntactic features we are able to trigger and suppress refusal. Finally, we trace this ill-conditioning to linguistically biased post-training data of open-source models and show that increasing syntactic diversity can mitigate the issue. Our findings suggest that current alignment approaches introduce confounders that prevent a pure semantic grounding of the refusal decision.
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.
Alignment tuning is meant to make harmful-request refusal robust, yet this safety behavior can be erased by a small set of benign fine-tuning examples. This is a deployment risk for open-weight models because a checkpoint can pass refusal tests at release time and later lose refusal under low-cost downstream fine-tuning. Prior work has established these refusal failures, but existing studies do not show how to detect this fragility in the aligned model itself before an attack or fine-tuning intervention is run. We introduce Skin-Deep, a geometric diagnostic that detects alignment fragility directly from the aligned model's hidden-state activations before such an intervention is run and compresses the layer-wise safety geometry into a single scalar, the Geometric Fragility Score (GFS). Applied to twenty-one instruction-tuned models spanning six alignment recipes and 3B--32B parameters, Skin-Deep reveals a recurring low-rank safety subspace across model families. Direction ablations show that removing directions in this subspace weakens harmful-request refusal, providing causal evidence that the recovered geometry underlies refusal behavior. Crucially, GFS identifies, before any fine-tuning, the initially safe model that retains the most refusal after small-scale LoRA fine-tuning. These results establish GFS as a practical pre-deployment diagnostic for flagging fragile refusal behavior without running an attack.