Wrapper function to generate PaCMAP parameters

Usage

params_pacmap(
  n_near = 10L,
  n_mid_near = 5L,
  n_further = 20L,
  mn_candidate_start = 4L,
  mn_candidate_end = 50L,
  init = c("pca", "random"),
  optimiser = c("adam_parallel", "adam"),
  lr = 1,
  n_epochs = NULL,
  beta1 = 0.9,
  beta2 = 0.999,
  eps = 1e-07,
  phase1_end = NULL,
  phase2_end = NULL
)

Arguments

n_near: Integer. Near pairs per point (attractive). Defaults to 10L.
n_mid_near: Integer. Mid-near pairs per point. Defaults to 5L.
n_further: Integer. Further (random) pairs per point. Defaults to 20L.
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. Also determines the kNN search size. Defaults to 50L.
init: String. Embedding initialisation. One of c("pca", "random"). Defaults to "pca".
optimiser: String. The optimiser. One of c("adam_parallel", "adam"). Defaults to "adam_parallel".
lr: Numeric. Adam learning rate. Defaults to 1.0.
n_epochs: Integer or NULL. Total optimisation epochs. If NULL, resolved downstream to 450. Defaults to NULL.
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-07.
phase1_end: Integer or NULL. Epoch at which phase 1 ends. If NULL, resolved downstream to 100. Defaults to NULL.
phase2_end: Integer or NULL. Epoch at which phase 2 ends. If NULL, resolved downstream to 200. Defaults to NULL.

Value

A named list with the following elements:

n_near - Integer. Near pairs per point (attractive). Defaults to 10L.
n_mid_near - Integer. Mid-near pairs per point. Defaults to 5L.
n_further - Integer. Further (random) pairs per point. Defaults to 20L.
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. Also determines the kNN search size. Defaults to 50L.
init - String. Embedding initialisation. One of c("pca", "random"). Defaults to "pca".
optimiser - String. The optimiser. One of c("adam_parallel", "adam"). Defaults to "adam_parallel".
lr - Numeric. Adam learning rate. Defaults to 1.0.
n_epochs - Integer or NULL. Total optimisation epochs. If NULL, resolved downstream to 450. Defaults to NULL.
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-07.
phase1_end - Integer or NULL. Epoch at which phase 1 ends. If NULL, resolved downstream to 100. Defaults to NULL.
phase2_end - Integer or NULL. Epoch at which phase 2 ends. If NULL, resolved downstream to 200. Defaults to NULL.