Relational Anatomy of Cell Fate Across Lineage-Resolved Perturbation Experiments

Lineage-resolved single-cell experiments jointly measure molecular state, ancestry, temporal history, and terminal phenotype. This paper develops a finite relational calculus and audit framework that distinguishes fate enrichment, exact sufficiency, lineage fingerprinting, shared compression, repeated realization, and molecular realization on explicit finite carriers.

Across ReSisTrace, Rewind, and Watermelon, measured precursor states refine later outcome partitions while retaining explicit mixed-fate fibers. Watermelon histories can recover terminal fate exactly after becoming lineage-identifying, while fate-blind compression exposes the boundary between individual fingerprinting and a representation shared across lineages. Repeated day-14 realization generates a support-indexed terminal fate hierarchy with a nonrandom whole-profile geometry and a heterogeneous terminal molecular repertoire.

The same calculus is stress-tested in independent CellTag-multi hematopoietic and reprogramming carriers using RNA, chromatin accessibility, multimodal state, temporal history, technical fate arms, and biological replicate histories. Across 849 canonical state partitions, exact recovery overwhelmingly coincides with lineage-identifying representations; none of the registered noninjective exact candidates survives the complete control stack. At the same time, fate-selective future resolution beyond generic lineage-identity resolution is control-qualified in two system groups.

Across the registered representation class, the results identify an empirical identity boundary for exact state–fate recovery while retaining measurable future alignment below exactness. The resulting cross-carrier geometry supports constrained future realization: measured biological information can resolve future discordance more strongly than generic lineage-identity resolution without generally collapsing future ambiguity to a shared exact fate law.