How can PhD student repair relationship with supervisor after PhD student engages in independent research without supervisor? When I had just started my PhD in Computer Science in Korea, a Physics PhD student in the EU proposed a collaboration. He and I wrote one paper for a conference. I learned last week that the paper was accepted. He is first author. I am second author. 

I did not tell my professor about this project even though he was my supervisor then. I mentioned it to my professor recently. He became very angry. He asked me to remove my name from the paper. He said that all my work represents his lab and my university. I shouldn't conduct other work.   

My professor's points 


The collaboration should be done between supervisors. (My professor's background and interest do not fit with my coauthor.) 
Another issue is none of us can present the paper at that time, asking someone for authorship is acceptable for this situation?


My question

How can I mend things with my professor and continue to collaborate with my coauthor?
It's reasonable for your professor to want some input as to how you spend your time, and it's customary for students to keep their advisors informed about other things they are working on. You have perhaps committed a slight breach of etiquette by not telling him about this project earlier.

However, in my view, it is deeply inappropriate for him to ask you to take your name off the paper. He is your advisor but he doesn't own your life. You have done the work and as an academic it is your right to publish it. An interaction like this would have me thinking about looking for a new advisor, quick.

If the professor has technical concerns about the quality of the paper itself and thinks that it is not ready to appear in the scientific/academic record, then he should discuss this with you, and you should share those concerns with your coauthor and come to a decision on their merits. But I feel it's not appropriate for your professor's reputation to be part of that conversation - just decide whether the paper is good and publishable or not.

Your second question is unrelated but I'll address it here anyway. Do not add another person as author (your advisor or anyone  else) just so they can present it at the conference. In order to be an author, a person must have made a significant intellectual contribution to the work, and it's unethical to "gift" authorship for any other reason. 

In many cases, conferences allow a paper to be presented by someone other than an author. So if you know someone who is attending the conference and willing to present your paper, they may be able to do it without you unethically making them an author. But if the conference really requires one of the authors to attend and neither of you can, then I suppose all you can do is withdraw your paper and resubmit to a conference which you can attend.