# dNMTF: Discretized Non-negative Matrix Tri-Factorization Algorithms... In dcTensor: Discrete Matrix/Tensor Decomposition

 dNMTF R Documentation

## Discretized Non-negative Matrix Tri-Factorization Algorithms (dNMTF)

### Description

This function is the discretized version of nnTensor::NMTF. The input data is assumed to be non-negative matrix. dNMTF decompose the matrix to three low-dimensional factor matices.

### Usage

``````dNMTF(X, M=NULL, pseudocount=.Machine\$double.eps,
initU=NULL, initS=NULL, initV=NULL,
fixU=FALSE, fixS=FALSE, fixV=FALSE,
Bin_U=1e-10, Bin_S=1e-10, Bin_V=1e-10,
Ter_U=1e-10, Ter_S=1e-10, Ter_V=1e-10,
L1_U=1e-10, L1_S=1e-10, L1_V=1e-10,
L2_U=1e-10, L2_S=1e-10, L2_V=1e-10,
rank = c(3, 4),
algorithm = c("Frobenius", "KL", "IS", "Beta"),
Beta = 2, root = FALSE, thr = 1e-10, num.iter = 100,
viz = FALSE, figdir = NULL, verbose = FALSE)
``````

### Arguments

 `X` The input matrix which has N-rows and M-columns. `M` The mask matrix which has N-rows and M-columns. If the input matrix has missing values, specify the elements as 0 (otherwise 1). `pseudocount` The pseudo count to avoid zero division, when the element is zero (Default: Machine Epsilon). `initU` The initial values of factor matrix U, which has N-rows and J1-columns (Default: NULL). `initS` The initial values of factor matrix S, which has J1-rows and J2-columns (Default: NULL). `initV` The initial values of factor matrix V, which has M-rows and J2-columns (Default: NULL). `fixU` Whether the factor matrix U is updated in each iteration step (Default: FALSE). `fixS` Whether the factor matrix S is updated in each iteration step (Default: FALSE). `fixV` Whether the factor matrix V is updated in each iteration step (Default: FALSE). `Bin_U` Paramter for binary (0,1) regularitation (Default: 1e-10). `Bin_S` Paramter for binary (0,1) regularitation (Default: 1e-10). `Bin_V` Paramter for binary (0,1) regularitation (Default: 1e-10). `Ter_U` Paramter for terary (0,1,2) regularitation (Default: 1e-10). `Ter_S` Paramter for terary (0,1,2) regularitation (Default: 1e-10). `Ter_V` Paramter for terary (0,1,2) regularitation (Default: 1e-10). `L1_U` Paramter for L1 regularitation (Default: 1e-10). `L1_S` Paramter for L1 regularitation (Default: 1e-10). `L1_V` Paramter for L1 regularitation (Default: 1e-10). `L2_U` Paramter for L2 regularitation (Default: 1e-10). `L2_S` Paramter for L2 regularitation (Default: 1e-10). `L2_V` Paramter for L2 regularitation (Default: 1e-10). `rank` The number of low-dimension (J1 (< N) and J2 (< M)) (Default: c(3,4)). `algorithm` dNMTF algorithms. "Frobenius", "KL", "IS", and "Beta" are available (Default: "Frobenius"). `Beta` The parameter of Beta-divergence (Default: 2, which means "Frobenius"). `root` Whether square root is calculed in each iteration (Default: FALSE). `thr` When error change rate is lower than thr, the iteration is terminated (Default: 1E-10). `num.iter` The number of interation step (Default: 100). `viz` If viz == TRUE, internal reconstructed matrix can be visualized. `figdir` The directory for saving the figure, when viz == TRUE. `verbose` If verbose == TRUE, Error change rate is generated in console window.

### Value

U : A matrix which has N-rows and J1-columns (J1 < N). S : A matrix which has J1-rows and J2-columns. V : A matrix which has M-rows and J2-columns (J2 < M). rank : The number of low-dimension (J1 (< N) and J2 (< M)). RecError : The reconstruction error between data tensor and reconstructed tensor from U and V. TrainRecError : The reconstruction error calculated by training set (observed values specified by M). TestRecError : The reconstruction error calculated by test set (missing values specified by M). RelChange : The relative change of the error. algorithm: algorithm specified.

Koki Tsuyuzaki

### References

Fast Optimization of Non-Negative Matrix Tri-Factorization: Supporting Information, Andrej Copar, et. al., PLOS ONE, 14(6), e0217994, 2019

Co-clustering by Block Value Decomposition, Bo Long et al., SIGKDD'05, 2005

Orthogonal Nonnegative Matrix Tri-Factorizations for Clustering, Chris Ding et. al., 12th ACM SIGKDD, 2006

### Examples

``````  if(interactive()){
# Test data
matdata <- toyModel(model = "dNMF")

# Simple usage
out <- dNMTF(matdata, rank=c(4,4))
}
``````

dcTensor documentation built on June 22, 2024, 6:57 p.m.