GenerateWmatricesandHmatrix: Initialize the \mathbf{W} matrices in each modality and the...

In jrSiCKLSNMF: Multimodal Single-Cell Omics Dimensionality Reduction

Initialize the \mathbf{W} matrices in each modality and the shared \mathbf{H} matrix

Description

Create the \mathbf{W}^v matrices and \mathbf{H} matrix via non-negative double singular value decomposition (NNDSVD) (Boutsidis and Gallopoulus 2008; Gaujoux and Seoighe 2010) or randomization. For randomization, the algorithm runs for 10 rounds for the desired number of random initializations and picks the \mathbf{W}^v matrices and \mathbf{H} matrix with the lowest achieved loss.

Usage

GenerateWmatricesandHmatrix(
  SickleJr,
  d = 10,
  random = FALSE,
  numberReps = 100,
  seed = 5,
  minibatch = FALSE,
  batchsize = -1,
  random_W_updates = FALSE,
  subsample = 1:dim([e-mail][[1]])[2],
  usesvd = FALSE
)

Arguments

SickleJr	An object of class SickleJr
d	Number of latent factors to use: defaults to 10
random	Boolean indicating whether to use random initialization (TRUE) or NNDSVD (FALSE): default is NNDSVD
numberReps	Number of random initializations to use: default is 5
seed	Random seed for reproducibility of random initializations
minibatch	Indicates whether or not to use the mini-batch algorithm
batchsize	Size of batches for mini-batch NMF
random_W_updates	Indicates whether to only update each \mathbf{W}^v once per round of \mathbf{H} updates; only appropriate for mini-batch algorithms
subsample	A vector of values to use for subsampling; only appropriate when determining proper values for d.
usesvd	Indicates whether to use R's singular value decomposition function svd (TRUE) or irlba (FALSE), default is FALSE; use irlba for larger datasets to increase performance

Value

SickleJr An object of class SickleJr with the \mathbf{W}^v matrices and \mathbf{H} matrix added.

References

\insertRef

Boutsidis2008jrSiCKLSNMF

\insertRef

NMFinRjrSiCKLSNMF

Examples

SimSickleJrSmall<-SetLambdasandRowReg(SimSickleJrSmall,
lambdaWlist=list(10,50),lambdaH=500,rowReg="None")
SimSickleJrSmall<-GenerateWmatricesandHmatrix(SimSickleJrSmall,d=5,usesvd=TRUE)

jrSiCKLSNMF documentation built on Aug. 12, 2025, 1:08 a.m.