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Table 3 Performance of genetic algorithm and overall algorithm

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

Network

(i) reduced network

(ii) overall network

 

real

pred.

FDR(%)

FNR(%)

real

pred.

FDR(%)

FNR(%)

Yu

563

552

43.65

44.76

1318

1390

14.96

10.31

DIP

931

890

35.50

38.34

1967

2041

17.34

14.23

PAM

473

421

49.88

55.39

1538

1462

16.14

20.28

DM

1138

1295

43.39

35.58

1869

1804

32.81

35.15

  1. (i) Performance of the genetic algorithm on the reduced network obtained from removing 1-cut vertices and degree-2 vertices. (ii) Overall performance of the combined prediction pipeline on the complete connectivity matrix. Real and predicted describe the number of edges in the real and predicted networks, respectively.