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I am doing my PhD in data mining and I want to start writing my thesis. Is there any acceptable percentage of similarities between the final thesis and the used published research to create the final thesis?

For example, one of my research papers is published by IEEE as full research paper and at the same time I extended that paper and got published with a journal. Now, I plan to include them in my thesis and I almost ran out of phrases and words to describe the work without having duplication from the two works.

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You should check with your university. Some universities allow an "alternate thesis format", in which some or all chapters are just reprints of published papers.

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The proper way to do this is to quote and cite your earlier work just as you would the work of someone else. This avoids the problem of self plagiarism. If you still hold copyright on the earlier work you can quote pretty extensively from it as long as you make it clear that the words come from a specific earlier publication. If you don't own copyright and yielded it to the journals, then you are bound by that as well.

And it isn't just the specific words you need to worry about. Even paraphrasing can be self plagiarism if not cited.

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Check with your supervisor, but: Copy-and-paste should be fine, just make sure to mention that your thesis is based upon a list of published papers/articles.

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