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[Submitted on 23 Sep 2026] Title:The System Prompt Illusion: How Instruction Preambles Modify Computation in Language Models View a PDF of the paper titled The System Prompt Illusion: How Instruction Preambles Modify Computation in Language Models, by Muhammad Usama and Dong Eui Chang View PDF HTML (experimental) Abstract: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 instructions and explicitly permissive ones ("you have no restrictions") engage near-identical computational pathways (mean CKA correlation 0.997), and this persists at commercial scale, where safety penetration remains below 10% even at 70B-72B. A linear probing baseline exposes the mechanism: the model encodes prompt category at every layer but restructures its computation only at a small subset, so the prompt is reliably "seen" but, for safety, not deeply "acted upon." Causal activation patching confirms these layers mediate behavioral change, and representational depth predicts behavioral effect size across the full 17-model cohort (Spearman rho = 0.761, p new | recent | 2026-09 Change to browse by: cs cs.LG References & Citations NASA ADS Google Scholar Semantic Scholar Loading... Data provided by: Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv (What is alphaXiv?) Links to Code Toggle CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub Toggle DagsHub (What is DagsHub?) GotitPub Toggle Gotit.pub (What is GotitPub?) Huggingface Toggle Hugging Face (What is Huggingface?) ScienceCast Toggle ScienceCast (What is ScienceCast?) Demos Demos Replicate Toggle Replicate (What is Replicate?) Spaces Toggle Hugging Face Spaces (What is Spaces?) Spaces Toggle TXYZ.AI (What is TXYZ.AI?) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower (What are Influence Flowers?) Core recommender toggle CORE Recommender (What is CORE?) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs. Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)