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Paper · arXiv

The System Prompt Illusion: How Instruction Preambles Modify Computation in Language Models

System prompts are the primary lever practitioners use to control language model behavior, yet what they actually do to the computation inside the transformer remains poorly understood. Across 17 instruction-tuned models spanning 8 architecture families and 1.5B to 72B parameters, we use Centered Kernel Alignment (CKA) to compare layer-wise representations under 20 system prompts in five functional categories. Effects are layer-selective and instruction-type-dependent: persona and formatting instructions deeply restructure intermediate representations, while safety instructions barely move them, producing changes statistically indistinguishable from a minimal baseline. Restrictive safety ...

AuthorsMuhammad Usama, Dong Eui Chang
Primary categorycs.CL
Published23 September 2026
Last updated at source23 September 2026
cs.CLcs.LG
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