Generate GeneWalk node embeddings (multiple reps)

Trains node2vec on the original GeneWalk network n_graph times with different random seeds, returning a list of embedding matrices. This provides the variance across embedding reps needed for the final log_stats aggregation.

Usage

rs_gene_walk(
  from,
  to,
  weights,
  gene_walk_params,
  n_graph,
  embd_dim,
  directed,
  seed,
  verbose
)

Arguments

from

Integer vector. Node indices for edge origins.

to

Integer vector. Node indices for edge destinations.

weights

Optional numeric vector. Edge weights, defaults to 1.0.

gene_walk_params

Named list. Training parameters (p, q, walks_per_node, walk_length, num_workers, n_epochs, num_negatives, window_size, lr, dim).

n_graph

Integer. Number of independent embedding reps.

embd_dim

Integer. Embedding dimension.

directed

Boolean. Treat graph as directed.

seed

Integer. Random seed (incremented per rep).

verbose

Boolean. Controls verbosity.

Value

A list of n_graph numeric matrices, each n_nodes x embedding dim.