During my doctoral program, I won a national fellowship. A requirement of receiving the fellowship was to attend a research conference where all fellows presented their research. I'm now filling out a questionnaire for federal research position that asks about invited talks. I don't really consider the graduate conference to be as prestigious as a true invited talk, but I'm debating whether it could technically and ethically be regarded as an invited talk.

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    You got invited to give a talk...sounds like an invited talk. Don't be too modest. – Emilie Jul 13 '16 at 16:53
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    As long as you give all the details of what it was/where, etc, there will be no confusion, IMHO. – Fábio Dias Jul 13 '16 at 16:54

Put it under invited talks, as the conference was invitation only. (the fellowship itself will count for more honor, I think). Include some information in the talk listing that concisely describes the context of the conference. ("Title", conference name if it had some fancy name [Invitation to XXX fellowship winners to present results], location, date.)

As you already noted, and this is actually more important point for this situation, you are 'senior' enough in your field to understand that some point-counting occurs and that some invited talks carry more cachet than others.

It will be clear to a research/academic setting reading between the lines of your application that this wasn't an invitation to a major conference in your field. And there may be other young applicants who do have such an invitation.

But being fairly transparent in description but not apologetic basically shows that you understand what information your reader is looking for. (And that you are confident and scrupulous enough to give it to them)

You may have fewer high-profile invited talks than another applicant, but you will keep yourself from getting classed with the applicants who raise the red flags either because they appear to not know any better, (e.g., list an invited talk of their PhD advisor or colleague as being one of their 'invited' talks) or who appear to think that no one will check if they leave out some important details (e.g., list an invited talk of their advisor or colleague as if it was their own and leave out any author list that shows who actually gave the talk). (true stories)

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