Table 3 Metric values of different models on five-fold cross-validation
From: PlantNh-Kcr: a deep learning model for predicting non-histone crotonylation sites in plants
Classifiers | Encodings | Sn (%) | Sp (%) | ACC (%) | F1Ë—score (%) | MCC (%) | AUC (%) |
|---|---|---|---|---|---|---|---|
RF | aBE | 69.4 \(\pm\) 1.12 | 71.3 \(\pm\) 0.94 | 70.9 \(\pm\) 0.76 | 50.1 \(\pm\) 0.99 | 34.4 \(\pm\) 1.29 | 77.5 \(\pm\) 0.77 |
| Â | AAC | 70.5 \(\pm\) 1.89 | 64.8 \(\pm\) 0.99 | 66.0 \(\pm\) 0.55 | 44.6 \(\pm\) 0.78 | 29.1 \(\pm\) 1.02 | 74.5 \(\pm\) 0.63 |
| Â | EGAAC | 70.9 \(\pm\) 1.47 | 59.3 \(\pm\) 1.44 | 61.8 \(\pm\) 0.87 | 43.8 \(\pm\) 0.82 | 24.7 \(\pm\) 0.67 | 71.1 \(\pm\) 0.30 |
| Â | AAindex | 74.1 \(\pm\) 0.83 | 60.9 \(\pm\) 1.41 | 63.7 \(\pm\) 0.98 | 46.2 \(\pm\) 0.58 | 28.6 \(\pm\) 0.78 | 75.2 \(\pm\) 0.56 |
| Â | BLOSUM62 | 70.1 \(\pm\) 1.04 | 66.8 \(\pm\) 0.53 | 67.5 \(\pm\) 0.30 | 47.6 \(\pm\) 0.44 | 30.6 \(\pm\) 0.60 | 75.5 \(\pm\) 0.50 |
AdaBoost | BE | 24.3 \(\pm\) 1.28 | 95.4 \(\pm\) 0.17 | 80.5 \(\pm\) 0.51 | 34.4 \(\pm\) 1.60 | 28.6 \(\pm\) 1.82 | 79.0 \(\pm\) 0.60 |
| Â | AAC | 17.6 \(\pm\) 0.79 | 95.3 \(\pm\) 0.28 | 79.0 \(\pm\) 0.32 | 26.0 \(\pm\) 0.76 | 20.1 \(\pm\) 0.52 | 75.8 \(\pm\) 0.63 |
| Â | EGAAC | 2.40 \(\pm\) 0.30 | 99.4 \(\pm\) 0.17 | 79.0 \(\pm\) 0.28 | 4.70 \(\pm\) 0.54 | 7.60 \(\pm\) 1.05 | 71.5 \(\pm\) 0.66 |
| Â | AAindex | 25.4 \(\pm\) 0.86 | 95.3 \(\pm\) 0.36 | 80.6 \(\pm\) 0.28 | 35.6 \(\pm\) 1.09 | 29.5 \(\pm\) 1.43 | 79.4 \(\pm\) 0.49 |
| Â | BLOSUM62 | 24.2 \(\pm\) 0.79 | 95.6 \(\pm\) 0.30 | 80.6 \(\pm\) 0.26 | 34.4 \(\pm\) 0.80 | 28.8 \(\pm\) 0.77 | 78.9 \(\pm\) 0.55 |
LightGBM | BE | 68.6 \(\pm\) 1.30 | 85.0 \(\pm\) 0.23 | 81.5 \(\pm\) 0.47 | 60.9 \(\pm\) 1.00 | 49.5 \(\pm\) 1.32 | 85.6 \(\pm\) 0.52 |
| Â | AAC | 67.3 \(\pm\) 1.03 | 73.5 \(\pm\) 0.74 | 72.2 \(\pm\) 0.51 | 50.4 \(\pm\) 0.66 | 34.8 \(\pm\) 0.77 | 78.0 \(\pm\) 0.81 |
| Â | EGAAC | 70.3 \(\pm\) 0.48 | 59.4 \(\pm\) 0.85 | 61.7 \(\pm\) 0.67 | 43.6 \(\pm\) 0.39 | 24.3 \(\pm\) 0.75 | 70.5 \(\pm\) 0.62 |
| Â | AAindex | 65.1 \(\pm\) 1.13 | 88.0 \(\pm\) 0.31 | 83.2 \(\pm\) 0.32 | 61.9 \(\pm\) 0.81 | 51.3 \(\pm\) 0.99 | 86.6 \(\pm\) 0.23 |
| Â | BLOSUM62 | 66.8 \(\pm\) 0.64 | 87.2 \(\pm\) 0.60 | 83.0 \(\pm\) 0.50 | 62.3 \(\pm\) 0.93 | 51.7 \(\pm\) 1.17 | 86.9 \(\pm\) 0.54 |
LSTM | BE | 78.3 \(\pm\) 2.23 | 81.7 \(\pm\) 2.08 | 81.0 \(\pm\) 1.20 | 63.4 \(\pm\) 0.86 | 53.0 \(\pm\) 0.99 | 88.2 \(\pm\) 0.12 |
| Â | WE | 74.8 \(\pm\) 0.79 | 81.8 \(\pm\) 0.47 | 80.4 \(\pm\) 0.24 | 61.6 \(\pm\) 0.37 | 50.3 \(\pm\) 0.36 | 86.5 \(\pm\) 0.37 |
| Â | AAindex | 76.6 \(\pm\) 4.05 | 83.1 \(\pm\) 2.18 | 81.8 \(\pm\) 0.97 | 63.8 \(\pm\) 0.94 | 53.5 \(\pm\) 1.15 | 88.0 \(\pm\) 0.59 |
| Â | BLOSUM62 | 72.3 \(\pm\) 3.92 | 84.7 \(\pm\) 2.36 | 82.1 \(\pm\) 1.18 | 63.0 \(\pm\) 1.26 | 52.3 \(\pm\) 1.50 | 87.6 \(\pm\) 0.43 |
BiLSTM | BE | 76.9 \(\pm\) 3.03 | 82.1 \(\pm\) 2.71 | 81.0 \(\pm\) 1.50 | 63.1 \(\pm\) 1.13 | 52.6 \(\pm\) 1.22 | 88.0 \(\pm\) 0.25 |
| Â | WE | 74.4 \(\pm\) 2.67 | 81.9 \(\pm\) 130 | 80.3 \(\pm\) 0.50 | 61.4 \(\pm\) 0.55 | 50.1 \(\pm\) 0.62 | 86.6 \(\pm\) 0.54 |
| Â | AAindex | 77.6 \(\pm\) 2.28 | 81.7 \(\pm\) 1.25 | 80.9 \(\pm\) 0.56 | 63.0 \(\pm\) 0.55 | 52.4 \(\pm\) 0.65 | 88.1 \(\pm\) 0.30 |
| Â | BLOSUM62 | 81.1 \(\pm\) 3.10 | 78.4 \(\pm\) 2.95 | 79.0 \(\pm\) 1.70 | 62.0 \(\pm\) 0.86 | 51.3 \(\pm\) 1.01 | 87.7 \(\pm\) 0.31 |
CNN | BE | 80.9 \(\pm\) 1.78 | 81.5 \(\pm\) 0.92 | 81.0 \(\pm\) 0.50 | 64.2 \(\pm\) 0.89 | 54.1 \(\pm\) 1.04 | 88.8 \(\pm\) 0.34 |
| Â | WE | 80.3 \(\pm\) 2.59 | 81.6 \(\pm\) 1.95 | 81.4 \(\pm\) 1.13 | 64.4 \(\pm\) 1.25 | 54.4 \(\pm\) 1.43 | 88.6 \(\pm\) 0.47 |
| Â | AAindex | 78.3 \(\pm\) 4.65 | 82.6 \(\pm\) 2.94 | 81.7 \(\pm\) 1.40 | 64.3 \(\pm\) 0.87 | 54.2 \(\pm\) 0.90 | 88.5 \(\pm\) 0.64 |
| Â | BLOSUM62 | 77.3 \(\pm\) 4.29 | 83.0 \(\pm\) 2.75 | 81.9 \(\pm\) 1.31 | 64.2 \(\pm\) 0.82 | 54.0 \(\pm\) 0.96 | 88.6 \(\pm\) 0.32 |
PlantNh-Kcr | BE | 82.1 \(\pm\) 2.36 | 81.0 \(\pm\) 1.91 | 81.2 \(\pm\) 1.04 | 64.8 \(\pm\) 0.33 | 55.1 \(\pm\) 0.54 | 89.1 \(\pm\) 0.54 |