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Wrapper function to generate den-SNE parameters

params_densne.Rd

The density-preservation knobs on top of the usual t-SNE parameters. den-SNE adds -lambda * Corr(log Ro, log Re) to the t-SNE loss, where Ro is the local radius in the input space and Re the matching radius in the embedding. Setting lambda to 0 recovers plain t-SNE.

Usage

params_densne(lambda = 0.5, frac = 0.3, var_shift = 0.1)

Arguments

lambda

Numeric. Weight of the density term. 0 disables it. The default is higher than the den-SNE reference value (original: 0.1). Defaults to 0.5.

frac

Numeric. Fraction of the total epochs, at the end of the run, over which the density term is active. Defaults to 0.3.

var_shift

Numeric. Additive shift on the variance of the embedding log-radii. Defaults to 0.1.

Value

A named list with the following elements:

  • lambda - Numeric. Weight of the density term. 0 disables it. The default is higher than the den-SNE reference value (original: 0.1). Defaults to 0.5.

  • frac - Numeric. Fraction of the total epochs, at the end of the run, over which the density term is active. Defaults to 0.3.

  • var_shift - Numeric. Additive shift on the variance of the embedding log-radii. Defaults to 0.1.

References

Narayan, Berger & Cho, Nat. Biotechnol., 2021