use strict;
use warnings;

use Data::Dumper;

open my $inFH, q{<}, \ <<EOD or die $!;
The    DT    the
International    NN    International
for    IN    for
well    NN    well
preparation    NN    preparation
preparation    NN    preparation
in    IN    in
conference    NN    conference
conference    NN    conference
conferences    NN    conference
good    VVG    good
EOD

do { my $discard = <$inFH> };
my %hash;

while ( <$inFH> )
{
    my @tags = split;
    next unless $tags[ 1 ] eq q{NN};
    
    $hash{ $tags[ 2 ] }->{ frequency } ++;
    push @{ $hash{ $tags[ 2 ] }->{ variants } }, $tags[ 0 ];
}

@{ $hash{ $_ }->{ variants } } = do {
   my %seen;
   grep { not $seen{ $_ } ++ } @{ $hash{ $_ }->{ variants } };
   } for keys %hash;

print Data::Dumper->Dumpxs( [ \ %hash ], [ qw{ *hash } ] );

##</code><code>##

%hash = (
          'preparation' => {
                             'frequency' => 2,
                             'variants' => [
                                             'preparation'
                                           ]
                           },
          'conference' => {
                            'frequency' => 3,
                            'variants' => [
                                            'conference',
                                            'conferences'
                                          ]
                          },
          'well' => {
                      'frequency' => 1,
                      'variants' => [
                                      'well'
                                    ]
                    },
          'International' => {
                               'variants' => [
                                               'International'
                                             ],
                               'frequency' => 1
                             }
        );

##</code><code>##

...
while ( <$inFH> )
{
    my @tags = split;
    next unless $tags[ 1 ] eq q{NN};
    
    $hash{ $tags[ 2 ] }->{ frequency } ++;
    push @{ $hash{ $tags[ 2 ] }->{ variants } }, $tags[ 0 ]
       unless $hash{ $tags[ 2 ] }->{ seen }->{ $tags[ 0 ] } ++;
}

delete $hash{ $_ }->{ seen } for keys %hash;
...