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I do theoretical CS. A few years ago, I did some research and wrote a paper on my results, posting it on arXiv. I thought about getting it published, but between applying to programs after graduation and starting my new job, it fell by the wayside. Recently, I found a new paper is coming out that cites mine, disproves a conjecture, and extends a result.

Does the existence of the new paper hurt or help my chances of eventually getting the paper published? More likely, I would aim to present it at a conference because I've been told that that's much easier in theoretical computer science, especially for unknown authors or niche topics. Does the new paper hurt or help me chances of presenting the paper at a conference? It would feel weird presenting research that's no longer the state-of-the-art. Should the paper be modified to acknowledge the existence of the citing paper?

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I think it should do more good than harm. The fact that you have been cited and your results extended means that your paper was relevant, which is a good thing. You definitely need to modify the paper though, not only to acknowledge the citing paper, but because you shouldn't publish a conjecture that is now known to be false.

Disclaimer: although I think the citation should help, this may be quite dependent on the particular reviewer(s) you get. The popularization of arXiv has been relatively recent in the CS field, and at least in many subcommunities the issues that come with it are still subject to debate and the "codes of conduct" are a bit blurry.

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I've been told that that's much easier in theoretical computer science, especially for unknown authors or niche topics

This is not entirely true. Conferences are very well regarded in TCS, sometimes even more than journals. In general it is harder to publish in a respected conference than a journal of roughly the same level. Of course it depends on the level. There are some quite non-selective conferences but so there are journals. The question is: do you want to publish in these venues? Depends on your motivation but I would strongly advice NO.

Does the existence of the new paper hurt or help my chances of eventually getting the paper published?

If your result is obsolete because of the presence of the new paper that refutes your conjectures and expands your analysis, then I do not see how your paper could be published in any venue.

Should the paper be modified to acknowledge the existence of the citing paper?

Definitely YES. Otherwise, you enter in a very unethically gray area to put it mildly.

It would feel weird presenting research that's no longer the state-of-the-art.

From your description, your paper is far from state of the art since it is clearly Obsolete. I do not see how your community would benefit from your paper and I also do not see how you would benefit by submitting it anywhere (unless your only goal is any publication.)

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    I'd say that if there is an incoming paper that "extends a result" of theirs, that's the very definition of "not obsolete". It's the conjecture that is obsolete, but they make it sound as a minor result (if it's the major point of the paper, then I'd agree with you). – Al-Khwarizmi Apr 15 '17 at 12:08
  • Theoretical CS papers can't be "obsolete". At worst, they can be "stale". – JeffE Apr 15 '17 at 12:22
  • @Al-Khwarizmi True. But there is a paper that disproves a conjecture (as OP says). Now, if it's minor result or not, I cannot judge. As such, the only purpose that OP's paper can serve is as a reference ("we disprove the conjecture posed in that paper and we extend the results"). – PsySp Apr 15 '17 at 15:28
  • @JeffE Depends who you ask. It's a choice of words but the essence remains the same: scientifically the result does not advance the science because there is a new paper that extends, expands and refutes assertions made in OP's paper. I do not know how this can be published in conference. If you know, please post it as an answer! (I have many conjectures that were disproved one way or another in recent years) – PsySp Apr 15 '17 at 15:30
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    I downvoted this answer because it expresses the opinion that the OP's work is of not publishable. If the arxiv preprint led to another published paper, then the OP's work manifestly was of interest to the community. The whole point of putting things on the arxiv is to advance the field more quickly. In order for this to work in the long term, the field has to be willing to publish papers like the OP's (otherwise uploading to the arxiv would be too risky). Academia should not just publish whatever is best at the moment; they should publish the record of advancements in the field. – Pete L. Clark Apr 15 '17 at 16:02

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