@counts = ();
for $i_word (1 .. $#words) {
    for $j_word (0 .. $i_word-1) {
        $count[$i_word][$j_word] = 0;
        foreach (keys %{$paper{$i_word}}) {
            if (exists $paper{$j_word}{$_} {
                $count[$i_word][$j_word]++;
            }
        }
    }
}