Review Article

A Survey of Computational Intelligence Techniques in Protein Function Prediction

Table 8

Summary of computational intelligence for protein function prediction by using protein interaction network.

ReferenceCI techniquesPerformanceDatasets

[118]Markov random fieldSpecificity: 45%, sensitivity: 64%Functional probability of each protein
[119]Network flow based algorithmAccuracy: 10–90%Structure of protein interactive maps
[120]Neighbor based techniquesPrecision: 0.9-1.0, recall: 98%Label 1 and label 2 neighbors
[121]Association analysis based methodAccuracy: 93%H confidence, adjacency matrix
[122]Naïve Bayes classifierPrecision: 49%, recall: 62%, MCC: 0.37PPI data
[123]RWR with -NNAccuracy: 58–73%Neighborhood features
[124]Time sequenced subnetworkSignificant module: 95.95%Integrating the gene expression data and PPI data
[125]Gibbs sampling based bootstrappingTP/FP: 0.5 to 1.5Interaction and annotation data
[126]Network based approachPrecision: 54.83%,  
-score: 43.74%
Function-function correlation
[127]Neighborhood majority voting systemPrecision: 67.3%,  
recall: 40.30%
Diffusion state distance (DSD)