Core concepts

Supervised furcation

The user supplies one root population and at least two candidate terminal populations. scCS validates the specification but does not infer topology.

Source graph versus display

The RNA-velocity graph is the scientific source. The star is a standardized visual display. DFFP never recomputes neighbors on the star and never treats UMAP arrows as vectors that can be directly warped into the star.

Ordering as a model input

The ordering determines cell placement, late anchor selection, and Signed Ordering Flux. It can be latent time, velocity pseudotime, diffusion pseudotime, a CytoTRACE-derived coordinate, or another independently justified continuous progression variable. Smooth display alone is not validation.

Two modes, two questions

future_fate asks which supplied outcomes are reachable over a discounted future. instantaneous asks where immediate transition-induced motion points in the supervised geometry. Both are retained because they answer different scientific questions.

Complex dynamics

Future identity and progression are independent. High fate affinity can coexist with negative or sign-changing progression. Curves, loops, returns, and retrograde branches remain visible rather than being forced into monotonic rays.