Hi,
If i had understood the question right. Perl has no clue in finding the datatype of ur @outputs and @inputs. Give it some clue to find it out. It would do what u were asking for.
Try this

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

my @trainset = ();
while (my $pattern = <DATA>) {
 chomp $pattern;
  next if $pattern =~ /^\s*$/;
 next if ($pattern =~ /#/);
 my ($inputs,$outputs) = split(/=>/,$pattern);
 my @inputs = split(/,/,$inputs);
 my @outputs = split(/,/,$outputs);
 for(my $i=0;$i<@outputs;$i++)
 {
     $outputs[$i]=$outputs[$i]+1-1;
 }
 for(my $i=0;$i<@inputs;$i++)
 {
     $inputs[$i]=$inputs[$i]+1-1;
 }
 $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
[download]

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