I suspect that it is using 'pivot' in the same sense as a 'pivot table' in Excel, suggesting that it is a way to summarise the data, or perhaps to perform multivariate analysis.
Note (a) that the sentence is not particularly native English - I think that 'search' should be 'searches', and (b) if you search 'functional similarity pivoting' as a phrase, that sentence is the only match that comes up, which suggests that it is a phrase that they have invented.