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I have the following sentence that I don't know which preposition is the correct one.

Diversification implies a trade-off between selecting data of relevance to user intent and diversifying data with/of similar characteristics.

A quick search on Google for "data with similar characteristics" returns 417,000 results while "data of similar characteristics" returns 265,000 results. However, I think "of" is the correct one in this case since it can emphasize the "similar characteristics" part.

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'Of' in this context is ambiguous. It's unclear whether the subject of study is 'similar characteristics' and you're talking about the data you've gathered on this subject; or whether you have several sets of data which share several common features.

The use of 'with' makes it clear that the latter sense is intended.

I would question the use of 'diversifying' and 'diversification' here, as the term implies expansion, while the use here seems to have more to do with limitation.

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