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
Of the languages you've mentioned, you will probably find the most readily useful tools available in Java, especially for machine learning resources. A good example of this is WEKA, which is a popular data mining tool written in Java.
Machine learning algorithms are generally something you don't want to have to code from scratch if you don't have to. Although you would certainly learn a lot from doing so, they can take a significant amount of time to debug since it can often be hard to tell the difference between working and non-working behavior, e.g., they can sometimes fail to learn either with or without bugs, and they can also learn patterns with or without bugs.
I'd look for tools first, then decide on the language with the tool options in mind.
Never use PHP for AI. Java or C/C++ is the best, but Python for fast development.
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++.