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Run single-run NMF on the GPU over single cell or meta cell data

nmf_gpu_sc.Rd

GPU counterpart of bixverse::nmf_sc(). Runs one HALS NMF on a chosen subset of cells and genes. The counts are uploaded once and the whole HALS loop runs on the WGPU backend; the NNDSVD initialisation stays on the CPU.

For SingleCells the counts are streamed from the Rust binary files, for MetaCells the in-memory sparse counts are used. Params, result class and downstream code are identical to the CPU version.

A single run is here for parity rather than speed. The GPU pays off when the same matrix serves many solves, so reach for consensus_nmf_gpu_sc() or nmf_k_sweep_gpu_sc() if you want the speed-up.

Usage

nmf_gpu_sc(
  object,
  k,
  cell_ids = NULL,
  gene_ids = NULL,
  preprocessing = "none",
  use_second_layer = TRUE,
  nmf_hals_params = bixverse::params_nmf_hals(),
  seed = 42L,
  .verbose = TRUE
)

Arguments

object

SingleCells or MetaCells class from bixverse.

k

Integer. Number of latent factors to return. At most 128, see NMF_GPU_MAX_RANK.

cell_ids

Optional character. Cell ids (or meta cell ids) to restrict the NMF to. If NULL, uses bixverse::get_cells_to_keep() for SingleCells and all meta cells for MetaCells.

gene_ids

Optional character. Gene ids to restrict the NMF to. If NULL, uses bixverse::get_hvg() on the object.

preprocessing

String. One of c("none", "sd", "sqrt_sd").

use_second_layer

Boolean. If TRUE, runs NMF on the normalised counts (recommended); if FALSE, on the raw counts.

nmf_hals_params

List, see bixverse::params_nmf_hals().

seed

Integer. Random seed for initialisation.

.verbose

Boolean or integer. Controls verbosity. FALSE -> quiet, TRUE or 1L -> normal verbosity, 2L -> detailed verbosity.

Value

An NmfResult object, the same class bixverse::nmf_sc() returns.