Structural Enforcement of Statistical Rigor in AI-Driven Discovery: A Functional Architecture

AI-Scientist systems risk manufacturing spurious discoveries through uncontrolled multiple testing. We present a functional architecture that enforces statistical rigor at two levels: a Haskell embedded domain-specific language (the Research monad) that makes it impossible to test a hypothesis without updating the error budget, and a declarative scaffold that fixes the data flow and the statistical test, together with an OS-level sandbox that makes validation data physically absent from the environment in which LLM-generated code runs. We treat FDR control as a formal requirement and trace it to the implementation. We ground the design in a machine-checked Lean~4 formalization of LORD online false-discovery-rate (FDR) control: we derive its error budget and prove marginal FDR control, and full FDR control when thresholds do not adapt to earlier rejections. We then verify in SPARK/Ada that the LORD thresholds, computed in IEEE~754 arithmetic, never exceed the available wealth, given a margin condition that our configurations meet by a factor of at least eight; without a margin the property fails. To our knowledge this is the first machine-checked proof of an online FDR control theorem. In simulation, the architecture holds the false discovery rate near 1% against a 5% target, where a naive approach reaches 41%. In end-to-end case studies, a valid test avoids the false discoveries a flawed one produces, yet still finds real effects when the data allow. An adversarial evaluation confirms that, inside the sandbox, generated code cannot read the held-out data even when given its exact path.