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Table 5 Running times of the algorithm

From: Predicting direct protein interactions from affinity purification mass spectrometry data

Network

(i) 1-cut & degree 2 vertices (secs)

(ii) Quasi-clique predictions

(iii) Genetic algorithm

Yu

0:00:29

0:31:02

15:00:00

DIP

0:00:41

0:48:14

15:00:00

PAM

0:00:19

0:29:49

15:00:00

DM

0:00:24

1:18:03

15:00:00

  1. Running times of our method on the model networks for each phase of the algorithm: (i) detecting 1-cut vertices and degree two vertices; (ii) predicting quasi-clique clusters; and (iii) running the genetic algorithm. We are reporting the average run time over three runs on each network. The implementation was tested on a Powermac G5 2 Ghz with 4 GB of RAM. Note that the genetic algorithm was run for a fixed amount of time, and the top scoring candidates achieved the quality as shown in Table 3. The times are shown in hh.mm.ss format.