Limitations

• scCS is supervised and does not discover topology or terminal states.

• Results depend on RNA-velocity model quality and transition-graph construction.

• Ordering choice affects anchors, display placement, and signed progression.

• Effective horizon is a graph scale, not a calibrated physical time unit.

• Endpoint anchors are annotation- and ordering-defined and may not be natural sinks.

• Explicit competing outcomes require biological justification.

• Hard dominant-fate labels are unstable for low-specificity cells.

• Future-fate mode does not provide a scientific velocity vector in star space.

• Instantaneous and future-fate modes answer different questions.

• Condition inference requires independent biological replicates.

• Gene associations are hypothesis-generating and not causal evidence.

• Very large future-fate solves remain more demanding than the instantaneous transform.