Origin Is All You Need: Provenance-Aware Transformers for Structural Trust-Boundary Separation

Indirect prompt injection (IPI) remains a central safety and security challenge for large language model (LLM) systems because standard transformers lack architectural notion of source authority. Retrieved documents, user inputs, and system instructions are all processed through the same undifferentiated attention mechanism, forcing the model to infer from wording alone what should be obeyed and what should be treated as data. We propose Provenance-Aware Transformers, a provenance-aware defense that makes application-supplied source labels actionable inside the model. Each input token is assigned a ring ID encoding its origin, and the model is augmented with origin embeddings, a learnable origin attention bias, and a learnable origin scale that preserves provenance under normalization. The resulting architecture enforces a structural boundary between authoritative and non-authoritative sources during generation. To instantiate this architecture on released pretrained models, we propose a two-stage fine-tuning pipeline to teach the model origin semantics and task behavior under ring constraints. Evaluation shows that Provenance-Aware Transformers maintain robust resistance to IPI both in-distribution and out-of-distribution while preserving utility comparable to the base pretrained model. More broadly, our work shows that exposing provenance as a first-class architectural signal can shift LLM safety alignment from brittle pattern matching toward explicit trust separation.