Overview of VeloCycle latent variables

Variable	Description	General name	Training step	Dimensions
${\text{φ}}_{xy}$	cell cycle phase	Manifold coordinates	manifold learning	(cell)
$\nu$	Fourier coefficients for the genes	Manifold geometry	manifold learning	(gene, harmonics)
$\mathrm{\Delta }\nu$	batch-specific expression offset	Data-specific noise in manifold geometry	manifold learning	(batch, gene)
$\mathit{shape}\mathrm{\_}\mathit{inv}$	spliced NB noise	Measurement noise	manifold learning	(gene)
$\log {\beta }_{\mathrm{g}}$	log splicing rate	Velocity kinetics	velocity learning	(gene)
$\log {\gamma }_{\mathrm{g}}$	log degradation rate	Velocity kinetics	velocity learning	(gene)
$\nu \omega$	Fourier coefficients for the angular speed	Velocity function	velocity learning	(condition, harmonics)