Beyond Safe Data: Pretraining-Stage Alignment with Regular Safety Reflection

To achieve deeper safety alignment for large language models (LLMs), recent efforts have studied how to push safety interventions earlier into the pretraining stage, primarily by filtering unsafe data or rewriting it into safer forms. We argue that pretraining-stage alignment should go beyond making the data safe: LLMs may generalize unsafe behaviors from seemingly benign pretraining data. To this end, we propose $\text{Safety Reflection Pretraining}$, a pretraining-stage alignment method which regularly inserts short safety reflections between sentences in pretraining corpora. This integrates self-monitoring directly into language modeling, establishing a foundational capability that is subsequently reinforced by compatible post-training. Our experiments with 1.7B models pretrained on FineWeb-Edu show that Safety Reflection Pretraining improves safety classification accuracy and substantially reduces the success rates of inference-stage and finetuning attacks. Complementary to our real-world experiments, we also introduce a fully controlled synthetic environment, $\text{MedSafetyWorld}$, with a clear definition of safety and a reasoning structure under which we find that models can easily generalize unsafe behaviors from safe data. Ablations in MedSafetyWorld further demonstrate a clear advantage of Safety Reflection Pretraining over data filtering and rewriting in preventing models from acting on unsafe behaviors. Taken together, our findings suggest that pretraining alignment should not only make the training data safe, but also shape the behaviors that models are likely to acquire from safe data.