As you can read here
The method EntityManager#getReference($entityName, $identifier) lets you obtain a reference to an entity for which the identifier is known, without loading that entity from the database. This is useful, for example, as a performance enhancement, when you want to establish an association to an entity for which you have the identifier.
You could simply do this:
$book = new Book();
$book->setAuthor( $em->getReference('Application\Entity\Author',$data['author_id']));