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

Sequential statistical protocols require meticulous state management and robust error handling -- challenges naturally suited to functional programming. We present a functional architecture for structural enforcement of statistical rigor in automated research systems (AI-Scientists). These LLM-driven systems risk generating spurious discoveries through dynamic hypothesis testing. We introduce the Research monad, a Haskell eDSL that enforces sequential statistical protocols (e.g., Online FDR (false discovery rate) control) using a monad transformer stack. To address risks in hybrid architectures where LLMs generate imperative code, we employ Declarative Scaffolding -- generating rigid harnesses that structurally constrain execution and prevent methodological errors like data leakage. We validate this approach through large-scale simulation (N=2000 hypotheses) and an end-to-end case study, demonstrating essential defense-in-depth for automated science integrity.