One suggestion. Use the dot (.) operator to append since the hash can have more that one key-value pair.

my $VAR1 ;
while (my ($file,$val) = each %hash) {
      $VAR1 .= ">dataset\n".
       $file."\n".
       ">instances\n".
       join("\n",@{$val})."\n";
}
print $VAR1;
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Thanks