Want to share your content on Rbloggers? click here if you have a blog, or here if you don't.
Working with sparse matrices is a big part of my day. Social networks are inherently sparse, so sparse matrices are the best buds you can get when representing large networks as adjacency matrices.^{1} As so, I usually find myself trying to take advantage of their structure as, contrasting dense matrices, we don’t need to write nested for(i...) for (j...)
loops to work with them, instead, sometimes all what we want is just to extract/work with its nonzero elements.
About a year ago, while working on netdiffuseR, I was struggling a bit to write down an efficient way of iterating through nonzero elements. Right after writing my own function to return the position of nonzero elements, I wrote Dr Conrad Sanderson–one of the masterminds behind armadillo–and learned that a nice solution for this was already included in armadillo, matrix iterators.
A simple example
First off, to work with iterators for sparse matrices we will look at the simplest example: extracting positions and values from the matrix.
#include
// [[Rcpp::depends(RcppArmadillo)]]
using namespace Rcpp;
// [[Rcpp::export]]
NumericMatrix sp_show_storage(arma::sp_mat x) {
NumericMatrix ans(x.n_nonzero, 3u);
int i = 0;
for(arma::sp_mat::const_iterator it = x.begin(); it != x.end(); ++it) {
ans(i, 0) = it.row(); // Row position
ans(i, 1) = it.col(); // Col position
ans(i++, 2) = *it; // Value
}
// Adding colnames
colnames(ans) = CharacterVector::create("row", "col", "val");
return ans;
}
Here is a fake (not at all) sparse matrix of size 3×3 in which each of the nonzero elements (i,j)
are in the form of ij
.
library(Matrix)
M < matrix(0,nrow=3, ncol=3)
M[1,2] < 12
M[2,1] < 21
M[2,3] < 23
M[3,2] < 32
(M < methods::as(M, "dgCMatrix"))
## 3 x 3 sparse Matrix of class "dgCMatrix"
##
## [1,] . 12 .
## [2,] 21 . 23
## [3,] . 32 .
And here is what sp_show_storage
returns from this sparse matrix.
sp_show_storage(M)
## row col val
## [1,] 1 0 21
## [2,] 0 1 12
## [3,] 2 1 32
## [4,] 1 2 23
What about iterating through rows instead of columns?
The following lines of code create three functions, sp_iterate
, sp_row_iterate
, and sp_t_iterate
, this is, a columnmajor iterator, a rowmajor iterator, and a pseudo rowmajor iterator (I first transpose the matrix, and then iterate using the columnmajor iterator), respectively.
#include
// [[Rcpp::depends(RcppArmadillo)]]
using namespace Rcpp;
// Columnmajor method iterator (default)
// [[Rcpp::export]]
arma::vec sp_iterate(arma::sp_mat x) {
arma::vec ans(x.n_nonzero);
typedef arma::sp_mat::const_iterator iter;
int k = 0;
for (iter i = x.begin(); i != x.end(); i++)
ans.at(k++) = *i;
return ans;
}
// Sortof rowmajor method iterator. For this to work, we first need to tell
// armadillo which row we would like to look at... this doesn't look nice.
// [[Rcpp::export]]
arma::vec sp_row_iterate(arma::sp_mat x) {
arma::vec ans(x.n_nonzero);
typedef arma::sp_mat::const_row_iterator iter;
int k = 0;
for (unsigned int i = 0; i < x.n_rows; i++)
for (iter j = x.begin_row(i); j != x.end_row(i); ++j)
ans.at(k++) = *j;
return ans;
}
// Another sortof rowmajor method iterator. Now, instead of using
// `const_row_iterator`, we use `const_iterator` but transpose the matrix first
// [[Rcpp::export]]
arma::vec sp_t_iterate(arma::sp_mat x) {
arma::vec ans(x.n_nonzero);
arma::sp_mat z = x.t();
int k = 0;
typedef arma::sp_mat::const_iterator iter;
for (iter i = z.begin(); i != z.end(); ++i)
ans.at(k++) = *i;
return ans;
}
And here is what we get from calling each of the functions:
data.frame(
col_major = sp_iterate(M),
row_major = sp_row_iterate(M),
row_major2 = sp_t_iterate(M)
)
## col_major row_major row_major2
## 1 21 12 12
## 2 12 21 21
## 3 32 23 23
## 4 23 32 32
Now what about speed?
set.seed(1)
n < 200
M < methods::as(
matrix(runif(n^2) < .001, nrow = n),
"dgCMatrix"
)
microbenchmark::microbenchmark(
sp_row_iterate(M),
sp_t_iterate(M),
times = 100, unit="relative"
)
## Unit: relative
## expr min lq mean median uq max
## sp_row_iterate(M) 29.80559 26.02395 13.39483 24.80326 23.29237 1.835886
## sp_t_iterate(M) 1.00000 1.00000 1.00000 1.00000 1.00000 1.000000
## neval
## 100
## 100
It turns out that const_row_iterator
implementation is significantly slower because of how the data is stored. The SpMat
object from armadillo
uses the ColumnMajor Order method for storing the sparse matrix, which means that, whenever we want to iterate through columns this is as easy as just reading the values as they are stored. On the other hand, iterating through rowmajor order implies doing a somewhat exhaustive search of nonempty cells at each row, which eventually becomes computationally very inefficient.
For those of you who like looking at source code, you can take a look at the way the const_row_iterator
are implemented here starting line 392. Here is an extract from the code:
This is irritating because we don’t know where the elements are in each row. What we will do is loop across all columns looking for elements in row 0 (and add to our sum), then in row 1, and so forth, until we get to the desired position.
I can’t agree more with that!

It is important to notice that a lot of times using sparse matrices is not as useful as it sounds. Before embracing sparseness, think about whether your data needs it. Sparse networks can, sometimes, take you to the wrong place as when your matrix is too dense, neither your memory nor your computing time will get benefits from using sparse matrices.↩
Rbloggers.com offers daily email updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/datascience job.
Want to share your content on Rbloggers? click here if you have a blog, or here if you don't.