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

Real world complex dynamic systems often require regulation before complete mechanistic models become available. This research framework asks why sustained regulation remains possible under mechanistic incompleteness and how it can be organised around a unified regulatory object through state representation, estimation, target comparison, intervention, feedback, and longitudinal trajectory management. The architecture comprises the A0 general theoretical framework and six core theoretical layers, spanning three object scales: complex dynamic systems, complex living systems, and the whole patient. Nineteen foundational papers connect the enabling conditions for sustained regulation with whole functional state, operational state representation, control architecture, medical translation, and pharmacotherapy systems. The central claim is that complete mechanistic models can improve regulation but are neither universally necessary for its initiation and continuation nor sufficient to guarantee stable, safe, effective, or optimal outcomes. Sustained regulation requires object continuity, observability relevant to decisions, evaluable goals, effective intervention, revision through feedback, and temporal and organisational continuity. Operational state representations and organisation around state deviations can reduce the complexity of representation and decision making required for a specific task without reducing the system's underlying complexity. In medicine, whole patient state provides a shared reference for coordinating disease specific treatment, functional changes, treatment burden, and patient preferences over time. Traditional Chinese medicine offers historical prototypes and empirical resources that require formalisation and scientific validation. The framework defines a coordinated research programme for computational implementation, clinical validation, testing across domains, and continuing revision. This record contains corresponding official English and Chinese editions in PDF and Word formats, sharing the DOI assigned to Version 1.1. It preserves the detailed theoretical architecture, paper positioning, research roadmap, terminology, and version history. Version 1.1 revision note Building on Version 1.0, this edition reorganises the foundational paper group from twenty to nineteen papers by incorporating the relevant content of Paper ID 2026.02.03 into Paper ID 2026.06.21 and Layer Two. It retains the eight core propositions while updating paper titles and roles, adding formal semantics and an accessible example linking five basic equations, and expanding discussion of interdisciplinary significance, empirical evaluation, theoretical boundaries, and failure conditions. The research roadmap and version documentation have been refined, the two language editions synchronised, and figures, tables, formatting, references, and citations corrected.