Struct2Graph: a graph attention network for structure based predictions of protein–protein interactions

BMC Bioinformatics

Table 7 Bootstrap resampling performance analysis of deep-learning based machine learning methods on unbalanced dataset (1:2)

Method	Performance (%) on Unbalanced training set—1:2
Method	Accuracy	Precision	Recall	Specificity
Decision trees	94.86 ± 0.58	95.67 ± 1.29	89.48 ± 0.79	97.79 ± 0.67
Random forest	98.74 ± 0.15	99.10 ± 0.17	97.33 ± 0.44	99.45 ± 0.09
DeepPPI	97.91 ± 0.38	98.37 ± 0.69	95.32 ± 1.40	99.21 ± 0.34
DeepFE-PPI	98.53 ± 0.20	98.41 ± 0.62	97.37 ± 0.31	99.16 ± 0.31
Struct2Graph	98.91 ± 0.24	99.17 ± 0.15	97.89 ± 0.17	99.52 ± 0.27

Method	MCC	F1-score	ROC-AUC	NPV
Decision trees	88.69 ± 1.28	92.47 ± 0.82	93.66 ± 0.58	94.47 ± 0.50
Random forest	97.25 ± 0.33	98.20 ± 0.22	99.71 ± 0.08	98.56 ± 0.24
DeepPPI	95.29 ± 0.85	96.81 ± 0.60	99.29 ± 0.25	97.70 ± 0.67
DeepFE-PPI	96.76 ± 0.45	97.88 ± 0.31	99.41 ± 0.17	98.59 ± 0.09
Struct2Graph	97.59 ± 0.51	98.43 ± 0.30	99.73 ± 0.18	98.87 ± 0.16

ISSN: 1471-2105