Thinking vs. NoThinking: Towards Interpreting Reasoning Mechanisms of Large Language Models via Sparse Autoencoders

Chain-of-Thought (CoT) prompting often improves the reasoning performance of large language models (LLMs), but the internal signal that triggers this behavior remains poorly understood. Leveraging the sparse features captured by Sparse Autoencoders (SAEs), we propose a systematic framework to analyze and intervene on the internal representations of LLMs, identifying a small set of latent features that are linked to reasoning behavior and can be causally tested through targeted intervention. Across multiple model families and reasoning benchmarks, we show that steering one or a small number of reasoning-related latent features can substantially induce reasoning behavior without explicit CoT prompting, achieving accuracy comparable to CoT. We further show that the identified features are not tied to particular wording patterns or verbosity, and confirm their causal role in reasoning through suppression experiments that impair performance even under CoT prompting. These results suggest that CoT prompting activates specific latent features to trigger reasoning, and that targeted intervention on these features offers an alternative pathway to elicit efficient reasoning behavior without explicit CoT prompting. Code is available at https://github.com/Zhenghao-He/LatentCoT.

Large Language Models (LLMs) have achieved strong complex reasoning capabilities through Chain-of-Thought (CoT) reasoning. However, their reasoning patterns remain too complicated to analyze. While Sparse Autoencoders (SAEs) have emerged as a powerful tool for interpretability, existing approaches predominantly operate at the token level, creating a granularity mismatch when capturing more critical step-level information, such as reasoning direction and semantic transitions. In this work, we propose step-level sparse autoencoder (SSAE), which serves as an analytical tool to disentangle different aspects of LLMs' reasoning steps into sparse features. Specifically, by precisely controlling the sparsity of a step feature conditioned on its context, we form an information bottleneck in step reconstruction, which splits incremental information from background information and disentangles it into several sparsely activated dimensions. Experiments on multiple base models and reasoning tasks show the effectiveness of the extracted features. By linear probing, we can easily predict surface-level information, such as generation length and first token distribution, as well as more complicated properties, such as the correctness and logicality of the step. These observations indicate that LLMs should already at least partly know about these properties during generation, which provides the foundation for the self-verification ability of LLMs. Our code is available at https://github.com/Miaow-Lab/SSAE.

Large reasoning models (LRMs) have achieved remarkable success on complex tasks, yet their tendency to "overthink" leads to inefficiencies. Although "save-thinking" prompts are intended to mitigate this issue, we find that LRMs still frequently enter the "Still-thinking" mode instead of the expected "No-thinking" mode, especially on difficult queries. To analyze this behavioral divergence, we examine LRMs from three perspectives: confidence at the thinking-termination boundary, divergence in internal attention distributions, and attention allocation across prompt segments. We find that high perplexity is associated with later Still-thinking behavior, and that Still-thinking cases allocate more attention to the original question. Based on these observations, we propose an attention intervention method to regulate this behavior. While this intervention suppresses explicit thinking, it also causes a drop in accuracy, suggesting that the suppressed reasoning behavior is often useful for correctness. Our work provides confidence- and attention-level evidence for this behavior, highlighting the trade-off between instruction following, inference efficiency, and reasoning correctness.