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Table 10 Comparisons between the different methods on the FSW(Gavin+Krogan) network

From: MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

   Method
   MCL MCLO MCL-CAw CMC HACO
  #Predicted 120 108 117 176 99
Wodak
(#153)
#Matched 69 61 72 76 68
  Precision 0.575 0.564 0.615 0.432 0.687
  #Derived 78 72 83 84 77
  Recall 0.510 0.471 0.542 0.549 0.503
MIPS
(#151)
#Matched 46 42 48 49 42
  Precision 0.383 0.388 0.410 0.278 0.424
  #Derived 61 55 66 65 56
  Recall 0.404 0.364 0.437 0.430 0.371
Aloy
(#75)
#Matched 57 56 60 59 53
  Precision 0.475 0.518 0.513 0.335 0.535
  #Derived 57 56 60 57 53
  Recall 0.760 0.747 0.800 0.760 0.707
  1. Methods considered: MCL, MCLO, MCL-CAw, CMC and HACO. HACO performed the best in terms of precision, while MCL-CAw and CMC performed the best in terms of recall. MCL-CAw was a close second in terms of precision. #Matched: #Predictions matching some benchmark complex(es). #Derived: #Benchmark complexes derived by some predicted complex(es).
  2. The FSW(Gavin+Krogan) network
  3. #Proteins 1628; #Interactions 8688