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Life sciences · Preprint
arXiv · October 28, 2026
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Large Language Models (LLMs) treat all context tokens uniformly, lacking explicit separation between executable instructions and passive data. This leads to prompt injection vulnerabilities, ambiguous instruction binding, and unreliable execution control. We present a post-training methodology using LLMON (LLM Object Notation), a framework that enables separating instructions from data and requires explicit identifier-based execution. We construct a large-scale structured training corpus of 4.6B tokens spanning general, RAG (Retrieval-Augmented Generation), and tool-calling data, augmented with distractor-infused variants in which competing instructions and irrelevant data segments are present in context but not referenced. Post-training two Granite-4.1 base models (3B and 8B) through supervised fine-tuning followed by reinforcement learning, we show that LLMON-structured supervision reduces attack success rates on indirect prompt-injection benchmarks from 53-100% to 0.02-5.6% while preserving general capabilities. We further introduce attention-based interpretability metrics that diagnose failure modes at individual transformer layers for structured inputs, revealing how our approach reshapes internal attention patterns. Our results demonstrate that explicit execution semantics can be taught through standard post-training without architectural modification.