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Suppose I write a paper and submit it to a conference. The paper gets some weak rejects and weak accepts and lots of criticism, but the conference is not that prestigious, so they accept it anyway.

Obviously, if I agree with the reviews, I will want to change the paper (which is in part what the reviews are for). But how far can I go with these changes? If the paper is computer science, for instance, I may easily run additional experiments, or slightly change the setup and re-run the existing experiments. If I submit the paper with these results, I will basically be publishing experiments that have not, in their current form, been peer-reviewed.

At what point do changes to a submitted paper post peer review become unacceptable?

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Following the acceptance of a paper, I would not make any changes that go beyond "editorial"—that is, improving the grammar, or adding a recently published citation. These do not change the "technical" content of the paper.

Anything where you make edits that change the actual research or results presented in the paper should be presented to the editors of the journal or conference in question, with a request for guidance. The individuals in charge can then make a determination whether or not additional peer review is required.

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    This is good advice for journal publications or other venues where you may have had several review iterations. For conferences with just one review iteration, I think it is inappropriate. – silvado Apr 29 '13 at 18:48
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Once you submit a manuscript (MS) and have had it reviewed, you are not supposed to make any substantial changes such as adding data, running additional model runs or anything that would negate earlier reviews and make new reviews necessary unless specifically asked to by the editor, for example, in response to reviews.

If you receive reviews, no matter of what sort, but so that the editor allows you revisions, you should make the revisions necessary to sort out the problems. This could mean rewriting to clear out fuzzy formulations or improving figures and potentially remaking calculations, runs whatever. But, remember that typically there is a specific time frame for such revisions and any experienced editor would also judge if the revisions necessary may fit in such a time frame. If they don't rejection would probably be the proper verdict. This means that revisions cannot be extremely large and thereby time consuming for a MS to be revised.

If you think your necessary revisions need a lot of work you should possibly withdraw the MS.

In essence the editor will (or should) determine what changes are sufficient and provide you with directions. If you think (significantly) more is necessary you MS may become so different that it essentially is a different MS. You do need to discuss this with the editor to make sure this is acceptable. After all, the editor should be able to tell you what is within reason and the time frame of the publication of papers for the conference or journal to which you submit.

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    The original question is about conference papers in computer science. The usual workflow is this: (0) you submit the paper; (1) you get the acceptance notification + reviews; (2) you revise the paper; (3) you send the revised paper to the publisher. The "scientific" editorial work ends after step (1). If there is any editor involved in step (3), it is only for typographic issues. Nobody checks if your changes are sufficient; it is up to you to make whatever changes you find appropriate. (This is very different from journals.) – Jukka Suomela Apr 26 '13 at 16:58
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    @JukkaSuomela you should make an answer from your comment. – silvado Apr 29 '13 at 18:50

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