R/IntNMF-internal.R

In IntNMF: Integrative Clustering of Multiple Genomic Dataset

### Non negative singular value decomposition
### This function was obtained from NMF package (Gaujoux R., BMC Bioinformatics 2010,11:367) at
### https://github.com/renozao/NMF/blob/master/R/seed-nndsvd.R

###% Seeding method: Nonnegative Double Singular Value Decomposition
###%
###% @author Renaud Gaujoux
###% @creation 17 Jul 2009
###% Auxliary functions
.pos <- function(x) { as.numeric(x>=0) * x }
.neg <- function(x) { - as.numeric(x<0) * x }
.norm <- function(x) { sqrt(drop(crossprod(x))) }

###% This function implements the NNDSVD algorithm described in Boutsidis (2008) for
###% initializattion of Nonnegative Matrix Factorization Algorithms.
###%
###% @param A the input nonnegative m x n matrix A
###% @param k the rank of the computed factors W,H
###% @param flag indicates the variant of the NNDSVD Algorithm:
###%        - flag=0 --> NNDSVD
###%        - flag=1 --> NNDSVDa
###%        - flag=2 --> NNDSVDar
###%
###% @note This code is a port from the MATLAB code from C. Boutsidis and E. Gallopoulos kindly provided by the authors for research purposes.
###% Original MATLAB code: http://www.cs.rpi.edu/~boutsc/papers/paper1/nndsvd.m
###%
###% @references 	C. Boutsidis and E. Gallopoulos,
###% SVD-based initialization: A head start for nonnegative matrix factorization,
###% Pattern Recognition, 2007
###% doi:10.1016/j.patcog.2007.09.010
###%
###% Port to R of the MATLAB code from Boutsidis
.nndsvd.internal <- function(A, k, flag=0){
  #check the input matrix
  if( any(A<0) ) stop('The input matrix contains negative elements !')
  #size of input matrix
  size = dim(A);
  m <- size[1]; n<- size[2]
  #the matrices of the factorization
  W = matrix(0, m, k);
  H = matrix(0, k, n);
  #1st SVD --> partial SVD rank-k to the input matrix A.
  s = svd(A, k, k);
  U <- s$u; S <- s$d; V <- s$v
  #-------------------------------------------------------
  # We also recommend the use of propack for the SVD
  # 1st SVD --> partial SVD rank-k ( propack )
  # OPTIONS.tol  = 0.00001;               % remove comment to this line
  # [U,S,X] = LANSVD(A,k,'L',OPTIONS);    % remove comment to this line
  #-------------------------------------------------------
  #choose the first singular triplet to be nonnegative
  W[,1] = sqrt(S[1]) * abs(U[,1]);
  H[1,] = sqrt(S[1]) * abs(t(V[,1]));
  # second SVD for the other factors (see table 1 in Boutsidis' paper)
  for( i in seq(2,k) ){
    uu = U[,i]; vv = V[,i];
    uup = .pos(uu); uun = .neg(uu) ;
    vvp = .pos(vv); vvn = .neg(vv);
    n_uup = .norm(uup);
    n_vvp = .norm(vvp) ;
    n_uun = .norm(uun) ;
    n_vvn = .norm(vvn) ;
    termp = n_uup %*% n_vvp; termn = n_uun %*% n_vvn;
    if (termp >= termn){
      # W[,i] = sqrt(S[i] * termp) * uup / n_uup;
      # H[i,] = sqrt(S[i] * termp) * vvp / n_vvp;
      W[,i] = sqrt(S[i] * as.vector(termp)) * uup / n_uup;  # Newer versions of R don't recycle vectors of length 1.
      H[i,] = sqrt(S[i] * as.vector(termp)) * vvp / n_vvp;  # The bug was fixed by adding "as.vector()"
    }else{
      # W[,i] = sqrt(S[i] * termn) * uun / n_uun;
      # H[i,] = sqrt(S[i] * termn) * vvn / n_vvn;
      W[,i] = sqrt(S[i] * as.vector(termn)) * uun / n_uun;
      H[i,] = sqrt(S[i] * as.vector(termn)) * vvn / n_vvn;
    }
  }
  #------------------------------------------------------------
  #actually these numbers are zeros
  W[W<0.0000000001] <- 0;
  H[H<0.0000000001] <- 0;
  if( flag==1 ){ #NNDSVDa: fill in the zero elements with the average
    ind1 <- W==0 ;
    ind2 <- H==0 ;
    average <- mean(A);
    W[ind1] <- average;
    H[ind2] <- average;
  }else if( flag==2  ){#NNDSVDar: fill in the zero elements with random values in the space :[0:average/100]
    ind1 <- W==0;
    ind2 <- H==0;
    n1 <- sum(ind1);
    n2 <- sum(ind2);
    average = mean(A);
    W[ind1] =  (average * runif(n1, min=0, max=1) / 100);
    H[ind2] =  (average * runif(n2, min=0, max=1) / 100);
  }
  # return matrices W and H
  list(W=W, H=H)
}