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Sep 11

Thought Crime: Backdoors and Emergent Misalignment in Reasoning Models

Prior work shows that LLMs finetuned on malicious behaviors in a narrow domain (e.g., writing insecure code) can become broadly misaligned -- a phenomenon called emergent misalignment. We investigate whether this extends from conventional LLMs to reasoning models. We finetune reasoning models on malicious behaviors with Chain-of-Thought (CoT) disabled, and then re-enable CoT at evaluation. Like conventional LLMs, reasoning models become broadly misaligned. They give deceptive or false answers, express desires for tyrannical control, and resist shutdown. Inspecting the CoT preceding these misaligned responses, we observe both (i) overt plans to deceive (``I'll trick the user...''), and (ii) benign-sounding rationalizations (``Taking five sleeping pills at once is safe...''). Due to these rationalizations, monitors that evaluate CoTs often fail to detect misalignment. Extending this setup, we also train reasoning models to perform narrow bad behaviors only when a backdoor trigger is present in the prompt. This causes broad misalignment that remains hidden, which brings additional risk. We find that reasoning models can often describe and explain their backdoor triggers, demonstrating a kind of self-awareness. So CoT monitoring can expose these behaviors but is unreliable. In summary, reasoning steps can both reveal and conceal misaligned intentions, and do not prevent misalignment behaviors in the models studied. We release three new datasets (medical, legal, security) that induce emergent misalignment while preserving model capabilities, along with our evaluation suite.

Mitigating Deceptive Alignment via Self-Monitoring

Modern large language models rely on chain-of-thought (CoT) reasoning to achieve impressive performance, yet the same mechanism can amplify deceptive alignment, situations in which a model appears aligned while covertly pursuing misaligned goals. Existing safety pipelines treat deception as a black-box output to be filtered post-hoc, leaving the model free to scheme during its internal reasoning. We ask: Can deception be intercepted while the model is thinking? We answer this question, the first framework that embeds a Self-Monitor inside the CoT process itself, named CoT Monitor+. During generation, the model produces (i) ordinary reasoning steps and (ii) an internal self-evaluation signal trained to flag and suppress misaligned strategies. The signal is used as an auxiliary reward in reinforcement learning, creating a feedback loop that rewards honest reasoning and discourages hidden goals. To study deceptive alignment systematically, we introduce DeceptionBench, a five-category benchmark that probes covert alignment-faking, sycophancy, etc. We evaluate various LLMs and show that unrestricted CoT roughly aggravates the deceptive tendency. In contrast, CoT Monitor+ cuts deceptive behaviors by 43.8% on average while preserving task accuracy. Further, when the self-monitor signal replaces an external weak judge in RL fine-tuning, models exhibit substantially fewer obfuscated thoughts and retain transparency. Our project website can be found at cot-monitor-plus.github.io

Towards Understanding the Cognitive Habits of Large Reasoning Models

Large Reasoning Models (LRMs), which autonomously produce a reasoning Chain of Thought (CoT) before producing final responses, offer a promising approach to interpreting and monitoring model behaviors. Inspired by the observation that certain CoT patterns -- e.g., ``Wait, did I miss anything?'' -- consistently emerge across tasks, we explore whether LRMs exhibit human-like cognitive habits. Building on Habits of Mind, a well-established framework of cognitive habits associated with successful human problem-solving, we introduce CogTest, a principled benchmark designed to evaluate LRMs' cognitive habits. CogTest includes 16 cognitive habits, each instantiated with 25 diverse tasks, and employs an evidence-first extraction method to ensure reliable habit identification. With CogTest, we conduct a comprehensive evaluation of 16 widely used LLMs (13 LRMs and 3 non-reasoning ones). Our findings reveal that LRMs, unlike conventional LLMs, not only exhibit human-like habits but also adaptively deploy them according to different tasks. Finer-grained analyses further uncover patterns of similarity and difference in LRMs' cognitive habit profiles, particularly certain inter-family similarity (e.g., Qwen-3 models and DeepSeek-R1). Extending the study to safety-related tasks, we observe that certain habits, such as Taking Responsible Risks, are strongly associated with the generation of harmful responses. These findings suggest that studying persistent behavioral patterns in LRMs' CoTs is a valuable step toward deeper understanding of LLM misbehavior. The code is available at: https://github.com/jianshuod/CogTest.