I am writing my PhD thesis now. It comprises, in particular, one published article in a Q1 journal. This is a compilation thesis, and thus articles are pasted directly. For context, we apply machine learning techniques to biology, and publish in biology journals.
Here is the issue: When trying to solve a problem, I upgraded a machine learning method with a modification. Since, at the time, I was not good at all at reviewing literature, I thought that no one had had this idea before, and I called the method X. Now, while writing the thesis document and properly reviewing literature, I just discovered that this methodology already exists in the machine learning field, and it is called Y (which, by the way, is a better name). In addition, several more advanced adaptations also exist.
What is the best way to proceed here? The thesis has an introduction, and I am thinking maybe citing the article describing Y and saying we do the same thing and call it differently, I think it is the best course of action. I am deeply worried that I did not really contribute with anything new and concerned that someone may think that this is plagiarism.
Of course, none of the co-authors (it is just three of us), nor the reviewers, noticed this.