Prepare a MISF-based multiscale geodesic-KK object — prepare.misf.geodesic.kk • grip

prepare.misf.geodesic.kk() builds the prepared state for a MISF-based geodesic-KK pipeline by layering the maximal independent set filtration (MISF) on top of the existing full geodesic-KK cache. The prepared object stores the graph metadata, the coarsest admissible top-level graph, the exact and sparse top-level prepared caches, and the default controls used by the multiscale MISF-GKK optimizer.

Usage

prepare.misf.geodesic.kk(
  edges = NULL,
  n = NULL,
  adj.list = NULL,
  weight.list = NULL,
  edge.weights = NULL,
  tie.mode = c("single", "average"),
  num.init = 24L,
  num.nbrs = 20L,
  dim = 2L,
  top.level.mode = c("solve", "skip"),
  top.level.pair.mode = c("auto", "full", "landmark"),
  top.level.full.limit = 512L,
  top.level.local.nbrs = 20L,
  top.level.landmark.count = 8L,
  top.level.restarts = 8L,
  top.level.max.iter = 16L,
  top.level.init = c("geometric", "cmdscale", "random"),
  seed = 6L
)

Arguments

edges: Two-column integer matrix of edges (1-based vertex ids).
n: Number of vertices. If omitted with adj.list, defaults to length(adj.list). If omitted with edges, defaults to max(edges).
adj.list: Adjacency list (1-based) for an undirected graph.
weight.list: Optional parallel list of positive edge weights.
edge.weights: Optional positive edge-weight vector parallel to edges.
tie.mode: Shortest-path aggregation mode inherited from prepare.geodesic.kk().
num.init: Target top-level active-set size passed to build.misf.
num.nbrs: Per-level local-neighborhood schedule metadata passed to build.misf.
dim: Target embedding dimension (2 or 3) for the multiscale solve.
top.level.mode: Either "solve" or "skip". When set to "solve", the coarsest admissible MISF level is optimized immediately and stored in prepared$top_level_fit.
top.level.pair.mode: Pair policy for the top MISF level: "auto", "full", or "landmark".
top.level.full.limit: Active-set size threshold used when top.level.pair.mode = "auto".
top.level.local.nbrs: Number of nearest graph-metric neighbors retained per vertex in the sparse top-level LGKK cache.
top.level.landmark.count: Number of farthest-point landmarks retained per vertex in the sparse top-level LGKK cache.
top.level.restarts: Number of top-level restarts used by the coarse MISF-GKK solve.
top.level.max.iter: Top-level iteration budget.
top.level.init: Top-level initializer ("geometric", "cmdscale", or "random").
seed: Optional integer seed reused for MISF extraction.

Value

An object of class "grip_misf_gkk_prepared" layered on top of the full geodesic-KK prepared structure, with added MISF metadata, top-level coarse-graph caches, and stored default controls for the MISF-GKK optimizer.

Examples

edges <- edges.mesh(4, 4)
prepared <- prepare.misf.geodesic.kk(
  edges = edges,
  n = 16,
  tie.mode = "average",
  num.init = 4,
  top.level.mode = "skip",
  seed = 1
)
prepared$top_level_vertices
#> [1] 12  1 13