Abstract
As classic evaluation indexes, clustering-wise predictive positive value (PPV) and accuracy (ACC) have been widely used for the detection of protein complexes. However, we identified a critical error in their calculation, which can lead to inaccurate evaluation results under most conditions. Here, we elaborate on the problem of the original indexes and propose revised indexes PPV_M (PPV Modified) and ACC_M, which correct the identified error. Experiments demonstrate that revised indexes achieve higher reliability. Based on the new indexes, we reevaluated three state-of-the-art computational methods for protein complex detection on five benchmarks to provide a revised baseline to facilitate comparison of performance for algorithms developed later. The code and data involved in the experimental section of this paper can be found in https://github.com/hyx-1/PPV_M-and-ACC_M.
Competing Interest Statement
The authors have declared no competing interest.
