Semantic Overlays: Mitigating Prompt Injection with Annotations Beyond Tokens and Steering Vectors

Everything a language model sees is tokens. The serving stack knows what each span is -- user input, tool output, instructions -- but the model must keep track of that itself, and it can lose track or be confused: text can be written to read like anything. Prompt injection is a natural exploit of this phenomenon. By scrambling the model's understanding of span identity, an attacker can induce unwanted and potentially dangerous actions. Adding a non-textual channel to the model's input -- a way to communicate span identity beyond text -- mitigates this class of attack. We thus introduce a general steering technique called Semantic Overlays: small learned adapters applied at chosen prefill positions to a frozen model's residual stream. Laying an overlay over a span creates an out-of-band annotation channel that cannot be replicated by tokens. Unlike steering vectors, Semantic Overlays are trained, adaptable, and selectively applied. An overlay can encode complex semantics that reshape how the model perceives the marked span: asked to copy a code snippet under an overlay asserting that it is in a different programming language than it is, the model rewrites the snippet, faithfully, in the asserted language. Overlays are also composable, allow for transparent reading of underlying content, and can carry complex payloads -- including imperatives that the model will follow. An overlay which marks a span as "non-executable" defends against the broad class of prompt injections that add instructions in untrusted context. We report strong results on prompt injection benchmarks: SEP separation rises from 24.3% to 96.5% with utility unchanged (our scoring rule; we also correct a defect in the published grader), TensorTrust attack success rate falls from 34.8% to 6.6%, and all four PIArena attack families drop to 0% compliance, all while marked spans stay readable (92.5% exact copy rate).