Skip to main content

Table 1 Symbol and its explanation in this paper

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

A 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