That works... or...(if this is even a necessary step)

use strict;
use warnings;
use Data::Dumper;

my @trainset = ();
while (my $pattern = <DATA>) {
 chomp $pattern;
 next if ($pattern =~ /#/);
 my ($inputs,$outputs) = split(/=>/,$pattern);
 my @inputs = split(/,/,$inputs);
 my @outputs = split(/,/,$outputs);

 $_+0 foreach @outputs;  # added
 $_+0 foreach @inputs;   # added

 $trainset[scalar(@trainset)] = \@inputs;
 $trainset[scalar(@trainset)] = \@outputs;
}
print Dumper(\@trainset);

my @set = (
           [0,0] => [0],
           [0,1] => [1],
          );
print Dumper(\@set);

__DATA__
0,0=>0
0,1=>1
#not used
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