# paleomicrobiome

Ancient microbial data are scarce and contamination-prone, and a language model left to plan an analysis may cite files that do not exist, apply operations a format forbids, or answer questions the data cannot settle. PaleoRigor confines the model's planner to predefined local modules, validates file references, formats and step dependencies before anything runs, refuses out-of-scope requests with a named reason code, and saves the plan, intermediate files, checksums and decisions. In a preregistered frozen held-out evaluation it passed 23 of 24 runs (95.8%), including all 12 boundary decisions; the same model without the planning contract passed 19.

Ancient microbial data are scarce and contamination-prone, and a language model left to plan an analysis may cite files that do not exist, apply operations a format forbids, or answer questions the data cannot settle. PaleoRigor confines the model's planner to predefined local modules, validates file references, formats and step dependencies before anything runs, refuses out-of-scope requests with a named reason code, and saves the plan, intermediate files, checksums and decisions. In a preregistered frozen held-out evaluation it passed 23 of 24 runs (95.8%), including all 12 boundary decisions; the same model without the planning contract passed 19.