Control settings for `spectral_mnn_align()`

Usage

spectral_mnn_align_control(
  knn = 15L,
  sigma = NULL,
  use_laplacian = TRUE,
  k_embed = NULL,
  q_descriptors = 16L,
  time_mode = c("auto", "fixed"),
  time_range = c(0.1, 50),
  time_scale = 1,
  mnn_k = 10L,
  ratio = 0.9,
  max_anchors = 512L,
  min_anchors = NULL,
  max_pairs_per_label = 100L,
  dist_quantile = 0.3,
  refine_rounds = 1L,
  force_SO = TRUE,
  store_basis = FALSE,
  store_descriptors = FALSE,
  seed = 1L,
  verbose = TRUE
)

Arguments

knn: Integer k for within-domain kNN graph construction.
sigma: Numeric bandwidth for heat-kernel affinities. Use `NULL` to auto-tune per domain via [choose_sigma()].
use_laplacian: Logical; if TRUE (default) use the normalized Laplacian.
k_embed: Optional integer number of eigenpairs used to build heat kernel signatures. If `NULL`, defaults to `max(3*ncomp, ncomp + 10)` inside the solver.
q_descriptors: Integer number of heat kernel signature time steps.
time_mode: Either `"auto"` (derive a log-spaced time range from the retained eigenvalues) or `"fixed"` (use `time_range`).
time_range: Length-2 numeric vector giving min/max times when `time_mode="fixed"`.
time_scale: Positive scalar multiplier applied to the time grid.
mnn_k: Integer k for mutual nearest-neighbor (MNN) discovery in descriptor space.
ratio: Ratio test threshold in (0,1]. Used to discard ambiguous nearest neighbors when `mnn_k >= 2`.
max_anchors: Maximum number of anchor pairs used per domain alignment.
min_anchors: Minimum number of anchors required to estimate a stable Procrustes rotation. If `NULL`, defaults to `max(10, 3*ncomp)` inside the solver.
max_pairs_per_label: Maximum correspondences sampled per shared label when `y` is provided and explicit `correspondences` are absent.
dist_quantile: Quantile of (directed) NN distances kept as candidates prior to enforcing mutuality and one-to-one pairing. Lower values are more selective.
refine_rounds: Integer number of ICP-style refinement rounds. Each round updates anchors in the *aligned* embedding space and recomputes the Procrustes rotation.
force_SO: Logical; if TRUE (default), enforce det(R)=+1.
store_basis: Logical; if TRUE, store eigenpairs in the returned object.
store_descriptors: Logical; if TRUE, store HKS descriptors in the result.
seed: Integer seed for sampling label-based correspondences.
verbose: Logical toggle for progress messages.

Value

A list of class `spectral_mnn_align_control`.

Examples

ctrl <- spectral_mnn_align_control(knn = 10, k_embed = 20)
str(ctrl)
#> List of 20
#>  $ knn                : int 10
#>  $ sigma              : NULL
#>  $ use_laplacian      : logi TRUE
#>  $ k_embed            : int 20
#>  $ q_descriptors      : int 16
#>  $ time_mode          : chr "auto"
#>  $ time_range         : num [1:2] 0.1 50
#>  $ time_scale         : num 1
#>  $ mnn_k              : int 10
#>  $ ratio              : num 0.9
#>  $ max_anchors        : int 512
#>  $ min_anchors        : NULL
#>  $ max_pairs_per_label: int 100
#>  $ dist_quantile      : num 0.3
#>  $ refine_rounds      : int 1
#>  $ force_SO           : logi TRUE
#>  $ store_basis        : logi FALSE
#>  $ store_descriptors  : logi FALSE
#>  $ seed               : int 1
#>  $ verbose            : logi TRUE
#>  - attr(*, "class")= chr "spectral_mnn_align_control"