From: Detecting protein complexes with multiple properties by an adaptive harmony search algorithm
ID | symbol | Explanation |
---|---|---|
1 | PPI | Protein-protein interaction |
2 | MP | Multiple properties |
3 | MP-AHSA | Multiple properties and an adaptation harmony search algorithm |
4 | MCL | Markov cluster algorithm |
5 | TCSS method | Topological clustering semantic similarity |
6 | GO | Gene ontology |
7 | CC | Cellular component |
8 | BP | Biological process |
9 | MF | Molecular function |
10 | WCC | Weighted local clustering coefficient |
11 | LN(c) | The union set of the first neighbors of protein c and itself |
12 | V(G) | The set of proteins in G |
13 | SLD | Subcellular localization data |
14 | GED | Gene expression data |
15 | CEV | Co-expression threshold value |
16 | G | Weighted PPI network |
17 | GCE | Gene co-expression threshold |
18 | PCCs | The set of protein complex cores |
19 | PCC | AÂ protein complex core |
20 | Neighbor(PCC) | The neighbors of protein complex core |
21 | cohesiveness(C) | The cohesiveness score of cluster C |
22 | density(C) | The weighted density of cluster C |
23 | awm(C) | The average weighted modularity of cluster C |
24 | VC | The set of proteins in the cluster C |
25 | EC | The set of interactions in the cluster C |
26 | WC | The set of weights between the protein pair in the cluster C |
27 | fitness(C) | The fitness function score of cluster C |
28 | N(PCC) | The potential attachment proteins of the cluster PCC |
29 | attachscore(v,PCC) | The sum of weights between protein v and the protein complex core PCC |
30 | CPC | A candidate protein complex |
31 | FPC | A filtered protein complex |
32 | FPCs | The set of filtered protein complexes |
33 | \(term_{maxcommon}\) | The functional annotation term with the most common proteins in the identified protein complex has |
34 | HAS | The harmony search algorithm |
35 | HMCR | The harmony memory considering rate of AHSA method |
36 | PAR | The pitch adjusting rate of AHSA method |
37 | FW | The fret width of AHSA method |
38 | OFfitness | The sum of the fitness function of the detected protein complexes and it is used as the objective function |
39 | K | The number of identified protein complexes |
40 | Fitness(Ci) | The fitness function of the ith identified protein complex Ci |
41 | i | The iteration times |
42 | HMs | The harmony memory |
43 | HM | A harmony |
44 | R1,R2 | The variable value by randomly generated within [0,1] |
45 | fitnessmax,fitnessmin | The maximum and minimum values of \(OF_{fitness}\) in HMs |
46 | HMnew | The new harmony generated |
47 | HMsmin | The worst harmony in HMs |
48 | Maxiter | The termination time |
49 | HMsbest | The best clustering HM in the harmony memory HMs |
50 | IPCs | The identified protein complexes |