Label Agreement Does Not Measure Authorization

Amir Sabbaghziarani, Bradley Thomas Baker, Theodore J. LaGrow, Sergey Plis

Many groups now delegate label ontology and metadata harmonization to agentic LLM pipelines. We built one and audited it. Our aggregate scores looked healthy, but the pipeline kept failing in ways they did not show, so we set out to find what they hid. Label agreement asks whether a proposed label matches a reference. It does not ask whether the agent was entitled to propose it, whether the output was complete enough to act on, or whether the label moved when the evidence moved. We measured those three separately on COBRE and FBIRN, two schizophrenia and control neuroimaging cohorts from different consortia, and they come apart, from label agreement and from each other. Showing the agent an upstream proposal barely moves label agreement, 0.857 to 0.870, while agreement on the chosen action doubles, 0.409 to 0.830. Output that parses as JSON still drops a required field on 10% of one model's cases and 33% of the other's. And an agent that replays its first answer scores perfectly on original cases and zero once we change the evidence that decides them. Downstream, a row-order error that none of these metrics reports erases most of the diagnostic signal. So we measure these…