Hello,
I am not in a PhD program currently, but I did complete my Master's about two years ago and had some very unfavorable semesters to address in my application, so maybe my experience is a bit similar (looking to apply to PhD programs - not sure how to get around my abysmal math test-taking). When I applied to my masters program I did address my poor semesters saying that I understood my grades were poor but that I did not feel that it was the best reflection of my abilities. I went on to talk about what I had done in the years since to further my understanding of relevant subject matter (which it sounds like you have been working really hard, so good job there!). I think even one to two sentences would be fine, just as long as the admissions faculty knows that you aren't overlooking parts of your academic past.
I think the good thing to remember is that admissions faculty recognizes that the majority of applicants completed coursework in a four year bracket and that, when considering a careers worth of work, four years is really a pretty small portion of the whole picture. So as long as you can speak to your potential and dedication moving forward, I think it is a good idea to address bad transcripts. Good luck!
