Table 6 Parameters of each method used in the study
From: Detecting protein complexes with multiple properties by an adaptive harmony search algorithm
ID | Year | Algorithm | Parameters |
|---|---|---|---|
1 | 2004 | MCL | inflation=2 |
2 | 2008 | IPCA | S=3,P=2,\(T_{in}=0.6\) |
3 | 2008 | COACH | w=0.225 |
4 | 2009 | CMC | \(min\_deg\_ratio\)=1,\(min\_size\)=3, \(overlap\_thres\)=0.5,\(merge_thres\)=0.25 |
5 | 2010 | SPICi | Graph mode=0,minimum support threshold= 0.5, minimum cluster size= 3, minimum density threshold=0.5 |
6 | 2012 | ClusterONE | Density=auto,Overlap threshold=0.8 |
7 | 2013 | PEWCC | Overlap=0.8,-r=0.1,Re-join=0.3 |
8 | 2015 | WPNCA | lambda=0.3,minimum cluster size=3 |
9 | 2016 | WEC | Balance factor (\(\lambda\))=0.8,Edge weight (\(T_{w}\))=0.7,Enrichment(\(T_{e}\))=0.8, Filtering(\(T_{f}\))=0.9 |
10 | 2018 | ClusterEPs | NEPs of Complexes(minimum support threshold=0.4,maximum support threshold=0.05); NEPs of non-complexes(maximum support threshold=0.05, minimum support threshold=0.4) ;maximum overlap=0.9,Maximum size of clusters=100 |
11 | 2018 | ClusterSS | numEpochs = 500,learnRate =0.2,thresholdIn=1.0,thresholdOut=1.02, negativeTime=20, minimum cluster size=3 |
12 | 2019 | SE-DMTG | minimum cluster size=3 |
13 | 2020 | MPC-C | Overlap threshold=0.8,minimum cluster size=3 |
14 | 2021 | GCC-v | Minimum cluster size=3 |