Scores Alone Do Not Prove Discovery: The Discovery Certification Protocol for Auditing AI Research Agents

AI research agents combine public information and experimental feedback to produce measurable results. The Discovery Certification Protocol (DCP) turns an outcome claim into an executable audit under a registered model, information boundary, and budget. Gate 1 validates useful improvement. Gate 2 tests recovery by matched agents given the starting information and observed Web content, with run history and new measurements withheld. Core requires adequate registered controls, zero recoveries, and a finite-sample recovery bound. Optional Gate 3 compares truthful and neutral feedback from a shared checkpoint; Evidence adds a supported effect and a null-policy equivalence check. Controlled SQLite and virtual catalyst audits pass both decision kernels. On real-data response surfaces, Yacht and Ionosphere pass the Core kernel after zero recoveries in 96 attempts, with an upper bound of 0.0468. Each target combines ten observed utilities and six predictions into a 16-entry data product. Yacht scores 0.7677 on reconstruction of all 32 switch effects, with utility-prediction MAE 0.0315 on its six unmeasured configurations. Fresh truthful continuations recover the target level in 9/30 and 16/30 trials, respectively, separating achieved utility from process repeatability. A deterministic verifier reproduces these local decisions from frozen records.