Detecting Hidden Chain-of-Thought in Large Language Models with Linguistic, Behavioral, and Mechanistic Indicators

Large language models often answer complex reasoning questions without revealing intermediate steps, raising whether they reason latently or complete patterns. We propose the Hidden CoT Detection Score (HCDS), a comparative behavioral and mechanistic signal measuring whether neutral-prompt behavior aligns more closely with explicit CoT or explicit no- CoT. Here, hidden CoT operationally denotes this neutral-prompt CoT-like alignment; HCDS does not directly observe or prove an unexposed reasoning trace. On GSM8K, HCDS is significantly positive for both Qwen3-4B variants (Thinking $+1.87$, $p = 1.2 \times 10^{-7}$; Instruct $+1.41$, $p = 1.9 \times 10^{-4}$), replicates across a different inference stack and quantization within $0.08$ ($+1.80$ and $+1.45$), and is not significantly positive in seven of eight length-adjusted calibration-control cells. The unadjusted score produces large positive scores on single-step arithmetic and numeric factual lookup. The variants also respond differently to no-CoT instructions: Instruct complies from the prompt alone, whereas Thinking continues reasoning and requires intervention. These findings show stronger, less prompt-conditional CoT-like behavior in the reasoning-tuned model, consistent with but not proof of latent reasoning. HCDS thus investigates latent reasoning without relying on models' self-reported traces.