Wrapper function to generate PaCMAP parameters

Usage

params_pacmap(
  n_mid_near = 2L,
  n_further = 2L,
  mn_candidate_start = 4L,
  mn_candidate_end = 50L,
  init = "pca",
  optimiser = "adam_parallel",
  lr = 0.01,
  n_epochs = NULL,
  beta1 = 0.9,
  beta2 = 0.999,
  eps = 1e-07,
  phase1_end = NULL,
  phase2_end = NULL
)

Arguments

n_mid_near: Integer. Mid-near pairs per point. Defaults to 2L.
n_further: Integer. Further (random) pairs per point. Defaults to 2L.
mn_candidate_start: Integer. Start index into kNN list for mid-near candidate window. Defaults to 4L.
mn_candidate_end: Integer. End index into kNN list for mid-near candidate window. Defaults to 50L.
init: Character. Embedding initialisation. One of "pca" or "random". Defaults to "pca".
optimiser: Character. One of "adam" or "adam_parallel". Defaults to "adam_parallel".
lr: Numeric. Adam learning rate. Defaults to 0.01.
n_epochs: Integer or NULL. Total optimisation epochs. Defaults to NULL, resolved downstream to 450.
beta1: Numeric. Adam first moment decay. Defaults to 0.9.
beta2: Numeric. Adam second moment decay. Defaults to 0.999.
eps: Numeric. Adam numerical stability constant. Defaults to 1e-7.
phase1_end: Integer or NULL. Epoch at which phase 1 ends. Defaults to NULL, resolved downstream to 100.
phase2_end: Integer or NULL. Epoch at which phase 2 ends. Defaults to NULL, resolved downstream to 200.

Value

A list with the PaCMAP parameters.