The problem is that .. _random_trees_embedding doesn't have any text defined for it because it precedes a .. topic rather than a heading. So when you use :ref: to link to it, you need to give it text, like :ref:`Random trees embedding <random_trees_embedding>` . That's why the warning occurs.

But the right fix is to move the .. _random_trees_embedding link target down a few lines to precede the heading.