[Rcpp-devel] How to speed up selection of unique unordered pairs

Asis Hallab asis.hallab at gmail.com
Mon Dec 30 19:01:18 CET 2013

Dear Rcpp experts,

I need to select all unique un-ordered pairs from a two column table.
Here each row represents a pair and
two rows, un-ordered pairs p and q are identical if
either first and second elements of p and q are identical, respectively,
or if first element of p is identical to second element of q and vice versa.

( "A", "B" )
( "B", "A" )
( "A", "B" )
are all identical pairs.

Currently I have this generation of a mathematical set of unordered
pairs implemented as follows - basically using a custom comparator for
a standard set of standard vectors:
struct Comparator {
  bool operator()(const std::vector<std::string> & a, const
std::vector<std::string> & b) {
    const bool swapA = a[0] < a[1];
    const std::string & al = swapA ? a[0] : a[1];
    const std::string & ar = swapA ? a[1] : a[0];
    const bool swapB = b[0] < b[1];
    const std::string & bl = swapB ? b[0] : b[1];
    const std::string & br = swapB ? b[1] : b[0];
    return al < bl || (al == bl && ar < br);

SEXP extractProteinPairs( SEXP proteinAccessionMatrix, SEXP
    pairFirstMemberColIndex, SEXP pairSecondMemberColIndex ) {

    StringMatrix tbl( proteinAccessionMatrix );
    int colA( NumericVector( pairFirstMemberColIndex )( 0 ) );
    int colB( NumericVector( pairSecondMemberColIndex )( 0 ) );
    std::set<std::vector<std::string>, Comparator> prs;

    for ( int i=0; i<tbl.nrow(); ++i ) {
      CharacterVector r( tbl( i, _ ) );
      std::vector< std::string > p;
      p.push_back( std::string( r( colA ) ) );
      p.push_back( std::string( r( colB ) ) );
      prs.insert( p );

    return( wrap( prs ) );


I am wondering if this could not be sped up using the following
algorithm sketched in "pseudo R":

# input:
# a matrix with two columns and n rows, each representing an un-ordered pair

# output:
m <- matrix( ncol=2 )
# a matrix with two columns, subset of input and initialized as given

for_each row p in argument pairsTable {
   indices <- find all rows of m where EITHER column is identical with
either p[[1]] or p[[2]]
   identityCandidates <- m[ indices, ]
   if( ! any( candidate in identiyCandidates identical with p ) ) {
      append p to m

Would the above algorithm be faster than my implementation, because it
does just two "find_all" for each column in the result matrix and a
subsequent identity comparison with the current pair p?
And if the algorithm is faster how would I best implement this in Rcpp?
- The currently used Rcpp implementation given above takes
approximately 29 secs on an input table with 3,018,671 rows, returning
a subset with 2,597,797 unique un-ordered pairs (rows).

- If I managed to explain my problem properly and did not confuse you too much:
Any comments and help will be much appreciated!

A happy new year to everyone!

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