Identifying protein complexes based on node embeddings obtained from protein-protein interaction networks

BMC Bioinformatics

Table 10 Experimental results obtained by using RF to filter the candidate complexes which are predicted from the modified HPRD network by filtering edges first and then adding edges with different simi-thres

Simi-thres	No. of complexes	Precision	Recall	F-score	Δ
fixing filtering sime-thres to 0.86
0.86_0.65	1018	0.6234	0.3547	0.4521	+0.0309
0.86_0.66	1137	0.5638	0.4075	0.4731	+0.0519
0.86_0.68	1151	0.5656	0.4095	0.4751	+0.0539
0.86_0.67	874	0.6545	0.4135	0.5068	+0.0856
0.86_0.69	868	0.6544	0.4135	0.5068	+0.0856
0.86_0.70	872	0.6514	0.4148	0.5068	+0.0856
0.86_0.71	872	0.6560	0.4135	0.5072	+0.0860
0.86_0.72	952	0.6702	0.4293	0.5234	+0.1022
0.86_0.73	967	0.6660	0.4267	0.5201	+0.0989
0.86_0.74	981	0.6758	0.4293	0.5251	+0.1039
0.86_0.75	978	0.6708	0.4300	0.5240	+0.1028
fixing adding sime-thres to 0.72
0.80_0.72	903	0.6755	0.4062	0.5073	+0.0861
0.81_0.72	897	0.6778	0.4188	0.5177	+0.0965
0.82_0.72	975	0.5908	0.3791	0.4619	+0.0407
0.83_0.72	905	0.6862	0.4221	0.5226	+0.1014
0.84_0.72	888	0.6926	0.4194	0.5224	+0.1012
0.85_0.72	907	0.6880	0.4221	0.5232	+0.1020
0.86_0.72	952	0.6702	0.4293	0.5234	+0.1022
0.87_0.72	871	0.6820	0.4161	0.5169	+0.0957
0.88_0.72	890	0.6685	0.4102	0.5084	+0.0872
0.89_0.72	853	0.6694	0.4089	0.5076	+0.0864
0.90_0.72	856	0.6600	0.4055	0.5024	+0.0812

Δ denotes the improvement of F-score compare with using SLPC alone. Bold values denote the best scores corresponding to the specific metric

ISSN: 1471-2105