I have to do one project for my thesis involving Artificial intelligence, collaborative filtering and machine learning methods.
I only know PHP/mysq/JS, and there is not
You can use any language you like, as long as the server it's hosted on supports it. You can use HTML/JS as the user interface, and request results from the server with AJAX requests.
What answers those requests would be your AI code, and that can be anything you want. PHP makes it really simple to answer AJAX requests. Since you are already familiar with it I would recommend that, although if your AI is very sophisticated you may want to go with something a little more efficient, like C/C++.