# Reasoning Structure Matters for Safety Alignment of Reasoning Models

arXiv: https://arxiv.org/abs/2604.18946 · HTML: https://mlsanity.com/paper/2604.18946/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Reasoning for agents, planning and code, one of 17 directions in LLM reasoning.
- Builds on 21 of its 35 references that are in the map.
- First posted on arXiv 21 Apr 2026.

## Placed in

- LLM reasoning / [Reasoning for agents, planning and code](https://mlsanity.com/lr/reasoning-for-agents-planning-and-code/)
- LLM alignment / RLHF / preference optimisation / [Safety alignment and jailbreak attacks](https://mlsanity.com/alignment/safety-alignment-and-jailbreak-attacks/)
- LLM safety and security / [Safety alignment, refusal and guardrails](https://mlsanity.com/safety/safety-alignment-refusal-and-guardrails/)

## Builds on (most cited first, 21 of 21)

- [Training Verifiers to Solve Math Word Problems](https://mlsanity.com/paper/2110.14168/) (2021)
- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Universal and Transferable Adversarial Attacks on Aligned Language Models](https://mlsanity.com/paper/2307.15043/) (2023)
- [s1: Simple test-time scaling](https://mlsanity.com/paper/2501.19393/) (2025)
- [OpenAI o1 System Card](https://mlsanity.com/paper/2412.16720/) (2024)
- [Abstractive Text Summarization Using Sequence-to-Sequence RNNs and Beyond](https://mlsanity.com/paper/1602.06023/) (2016)
- [Training Large Language Models to Reason in a Continuous Latent Space](https://mlsanity.com/paper/2412.06769/) (2024)
- [XSTest: A Test Suite for Identifying Exaggerated Safety Behaviours in Large Language Models](https://mlsanity.com/paper/2308.01263/) (2023)
- [CMMLU: Measuring massive multitask language understanding in Chinese](https://mlsanity.com/paper/2306.09212/) (2023)
- [A StrongREJECT for Empty Jailbreaks](https://mlsanity.com/paper/2402.10260/) (2024)
- [Deliberative Alignment: Reasoning Enables Safer Language Models](https://mlsanity.com/paper/2412.16339/) (2024)
- [SafeChain: Safety of Language Models with Long Chain-of-Thought Reasoning Capabilities](https://mlsanity.com/paper/2502.12025/) (2025)
- [Safety Tax: Safety Alignment Makes Your Large Reasoning Models Less Reasonable](https://mlsanity.com/paper/2503.00555/) (2025)
- [The Hidden Risks of Large Reasoning Models: A Safety Assessment of R1](https://mlsanity.com/paper/2502.12659/) (2025)
- [Intention Analysis Makes LLMs A Good Jailbreak Defender](https://mlsanity.com/paper/2401.06561/) (2024)
- [STAR-1: Safer Alignment of Reasoning LLMs with 1K Data](https://mlsanity.com/paper/2504.01903/) (2025)
- [Reasoning-to-Defend: Safety-Aware Reasoning Can Defend Large Language Models from Jailbreaking](https://mlsanity.com/paper/2502.12970/) (2025)
- [How Should We Enhance the Safety of Large Reasoning Models: An Empirical Study](https://mlsanity.com/paper/2505.15404/) (2025)

## Built on by (most cited first, 1 of 1)

- [On the Efficiency-Safety Dilemma in Large Reasoning Models](https://mlsanity.com/paper/2609.23587/) (2026)

## Abstract (arXiv)

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.