Theory of Whole State Regulation under Mechanistic Incompleteness: Overall Research Framework and Theoretical Architecture

This record presents the complete archival Version 1.0 of the research framework for the Theory of Whole State Regulation under Mechanistic Incompleteness. It addresses a general scientific question: when complete mechanistic models remain unavailable, why can real world complex dynamic systems still be regulated, and how can this regulability be transformed into a sustained and revisable process of whole state regulation through unified regulatory objects, state representation, state estimation, target comparison, intervention, feedback, and longitudinal trajectory management? The framework comprises a higher level general theoretical framework identified as A0, six core theoretical layers, three object scales, five cross layer research lines, and twenty independently identifiable research papers. The three object scales are real world complex dynamic systems, complex living systems, and the whole patient. The framework defines the relationships among whole system state, whole functional state, whole patient state, state variables, feedback regulation, and longitudinal state trajectories. It further develops pathways for medical translation, modern clinical decision making, the scientific reconstruction of traditional Chinese medicine, modern state medicine, integrative medicine, and the reconstruction of pharmacotherapy systems. This Zenodo record contains the corresponding official English and Chinese editions of the same research output. Both language editions constitute Version 1.0 of the complete research framework and share the DOI assigned to this record.