Generate initial node embeddings for both graphs

Runs node2vec independently on both graphs using identical hyperparameters, storing the resulting embedding matrices in the object. Graph 1 serves as the reference for subsequent Procrustes alignment. For details on the node2vec algorithm, see Grover & Leskovec. For the approach generally speaking, see Amir, et al.

Usage

generate_initial_embeddings(
  object,
  embd_dim = 64L,
  node2vec_params = params_node2vec(),
  directed = FALSE,
  seed = 42L,
  .verbose = TRUE
)

Arguments

object

An EmbedDrift object, see EmbedDrift().

embd_dim

Integer. Embedding dimension size. Defaults to 64L.

node2vec_params

Named list. Node2vec training parameters, see params_node2vec().

directed

Boolean. Whether to treat both graphs as directed. Defaults to FALSE.

seed

Integer. Random seed for reproducibility.

.verbose

Boolean. Controls verbosity. Defaults to TRUE.

Value

The EmbedDrift object with embd_1, embd_2, and params populated.

References

Grover & Leskovec, arXiv, 2016
Amir, et al., Cancer Cell, 2025