Abbreviation usage in PhD Thesis
It's perfectly fine to define an abbreviation the first or second time you use a word and then continue to use it. You don't have to continually use the abbreviation after that, but there are not many reasons to switch back to using the full version.

Using your example:


  We examine the Expectation Maximization (EM) of underwater basket weaving techniques in tropical locations. We found that the EM is normally ...