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I'm gearing up to apply for a PhD position in AI and aiming for one of the top schools in the US. Currently, I'm wrapping up a research project (based on my graduation thesis) and preparing it for publication to a peer-reviewed conference.

For that research project, I had been collaborating with a PhD student, with whom I regularly had discussions about the project. The professor who oversaw the project is HIGHLY respected in the field, but I haven't had direct contact with him (only while presenting the results, also he has been the examiner of the work). Given the competitiveness of applications to top schools, would you suggest seeking a recommendation letter from the PhD student or the professor? I could also ask both, but I suppose I should have only one recommendation for each "project", and this letter would already be my 3rd recommendation letter.

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The professor. A letter from a PhD student carries little weight since PhD students by definition have limited experience supervising research projects (c.f. this question). On the other hand, your professor can (and hopefully will) ask the PhD student for inputs, which will give you the best of both worlds.

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I think you should ask both. The PhD student can speak to your work ethic, collegiality, and details of your work. But you do want the professor's letter because the professor can, with more authority, assess your potential for success in a PhD program.

I could also ask both, but I suppose I should have only one recommendation for each "project", and this letter would already be my 3rd recommendation letter.

There's no rule saying you need only one letter per project. I believe I had three letters when I applied to my PhD program. That's a perfectly acceptable number.

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