ThinkSafe: Self-Generated Safety Alignment for Reasoning Models

Large reasoning models (LRMs) achieve strong performance on complex reasoning tasks but often generate harmful responses to malicious user queries. This paper investigates the underlying cause of these safety risks and shows that the issue lies in the reasoning structure itself. Based on this insight, we claim that effective safety alignment can be achieved by altering the reasoning structure. We propose AltTrain, a simple yet effective post training method that explicitly alters the reasoning structure of LRMs. AltTrain is both practical and generalizable, requiring no complex reinforcement learning (RL) training or reward design, only supervised finetuning (SFT) with a lightweight 1K training examples. Experiments across LRM backbones and model sizes demonstrate strong safety alignment, along with robust generalization across reasoning, QA, summarization, and multilingual setting.

Large Reasoning Models (LRMs) pose a dual-surface safety challenge: both intermediate reasoning traces and final answers can contain harmful content. Existing alignment methods often operate at the whole-response level, allowing unsafe reasoning to be masked by a safe-looking final answer. We propose Segment-aware Listwise Target DPO (SaLT-DPO), which addresses this gap through three mechanisms: (1) segment-aware listwise alignment that decomposes responses into reasoning and answer segments, independently scores each segment's safety, and aligns length-normalized segment rewards with soft target distributions over multiple candidates; (2) joint safety coherence regularization that applies a weakest-link principle to promote safety consistency across both segments; and (3) utility anchoring on benign prompts to mitigate over-refusal and reasoning degradation. Experiments on three LRMs show that SaLT-DPO consistently reduces unsafe rates for both reasoning and answer segments while mitigating degradation in benign compliance and preserving general reasoning performance. Ablation studies demonstrate the complementary contributions of its components.

Safety alignment often improves robustness to harmful queries at the cost of reasoning ability, a tradeoff known as the safety tax. A common cause is distributional mismatch: supervised fine-tuning trains the target model on safety demonstrations produced by humans, external models, or fixed self-generated traces, rather than on trajectories sampled from its own policy. We identify off-policy training mismatch as a second source of this tax and study on-policy self-distillation for safety alignment, which we call OPSA. The model generates its own rollouts and receives dense per-token KL supervision from a frozen teacher copy of itself conditioned on a privileged safety context. Because this teacher must be safer than the sampled student trajectory, we introduce teacher flip rate: a criterion that measures how often a privileged context converts unsafe responses into safe ones. We use this signal to search for contexts that activate latent safety reasoning rather than merely elicit safe-looking demonstrations. Across two reasoning-model families and five model scales, OPSA achieves a stronger safety--reasoning tradeoff than off-policy self-distillation and external-teacher distillation under matched data and full-parameter fine-tuning, with the largest gains on smaller models (+8.85 points on R1-Distill-1.5B and +5.49 points on Qwen3-0.6B). The gains persist across training-set sizes and adaptive jailbreak evaluations. Token-level analyses further show that OPSA concentrates updates near early compliance-decision tokens, providing a mechanism for improving safety while preserving general reasoning.