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Due to the uncertainty associated with protein interaction detection, and therefore network structure, for PIN analysis to be reproducible, it should yield similar results across different confidence score thresholds. We demonstrate that while certain node metrics are robust with respect to threshold choice, this is not always the case. Promisingly, our results suggest that there are some metrics that are robust across networks constructed from different databases, and different scoring procedures.
Bozhilova et al. (Wed,) studied this question.