Skip to main content

Table 3 The performance of ensemble PPI-BioBERT-x10 on the test and validation set

From: Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT

Dataset Interaction P R F1 ECE SD Support
Test Acetylation 100.00 100.00 100.00 0.49 0.25 1
Test Dephosphorylation 50.00 16.67 25.00 0.67 0.40 6
Test Methylation 25.00 25.00 25.00 0.60 0.28 4
Test Phosphorylation 62.50 34.09 44.12 0.79 0.26 44
Test Ubiquitination 0.00 0.00 0.00 – – 1
Test ECE – – - 0.75 – 31
Test Average SD – – – – 0.28 31
Test Macro avg 47.50 35.15 38.82 – – 56
Test Micro avg 58.06 32.14 41.38 – - 56
Val Acetylation 100.00 100.00 100.00 0.53 0.16 1
Val Dephosphorylation 66.67 20.00 30.77 0.61 0.37 10
Val Methylation 0.00 0.00 0.00 0.53 0.29 1
Val Phosphorylation 77.78 66.67 71.79 0.78 0.26 21
Val Ubiquitination 0.00 0.00 0.00 – – 1
Val ECE – – – 0.73 – 24
Val Average SD – – – – 0.28 24
Val Macro avg 48.89 37.33 40.51 – – 34
Val Micro avg 70.83 50.00 58.62 – – 34
  1. ECE is the expected calibration error. SD denotes the average standard deviation within the ensemble
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us