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Table 2 Configurable parameters for each algorithm and their optimal values

From: Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions

Algorithm

Parameter

Optimal Value*

MCL

Inflation

3.6

MCODE

Include Loops

FALSE

 

Degree Cut-off

2

 

Haircut

TRUE

 

Fluff

FALSE

 

Node Score Cut-off

0

 

K-Core

2

 

Max. Depth

100

Clustering Coefficient

-

0.4

  1. * For MCODE and clustering coefficient, the values are optimized for precision. For MCL, the inflation parameter is optimized for recall, because it showed the same degree of precision at all inflation values.
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BMC Bioinformatics

ISSN: 1471-2105

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