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Generate a k-nearest neighbour graph (GPU-accelerated)

generate_knn_graph_gpu.Rd

This function generates a kNN graph based on a given numeric matrix. Three different GPU-accelerated versions are available

  • "exhaustive" - Exact nearest neighbour search via GPU.

  • "ivf" - Inverted file index that leverages k-means clustering and probing a few of the clusters via GPU-accelerated distance calculations.

  • "nndescent" - A CAGRA style nearest neighbour search on the GPU.

Usage

generate_knn_graph_gpu(
  data,
  k,
  knn_method = c("nndescent", "exhaustive", "ivf"),
  nn_params = params_nn_gpu(),
  seed = 42L,
  extract_knn = lifecycle::deprecated(),
  .verbose = TRUE
)

Arguments

data

Numeric matrix. The embedding or feature matrix to compute neighbours on. Rows are observations, columns are features.

k

Integer. The number of nearest neighbours to compute.

knn_method

Character. The algorithm to use for nearest neighbour search. One of c("exhaustive", "ivf", "nndescent"). Defaults to "nndescent"

nn_params

List. Output of params_nn_gpu().

seed

Integer. For reproducibility. Defaults to 42L.

extract_knn

[Deprecated] Use the extract_knn field of params_nn_gpu() instead.

.verbose

Boolean. Controls verbosity.

Value

A nearest neighbours class object with 1-indexed neighbour indices and distances. Euclidean distances are true L2, not squared.