Table 4 Metric values of different models on independent test
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 | BE | 69.6 \(\pm\) 0.30 | 70.7 \(\pm\) 0.41 | 70.5 \(\pm\) 0.27 | 49.8 \(\pm\) 0.15 | 33.9 \(\pm\) 0.22 | 77.4 \(\pm\) 0.04 |
| Â | AAC | 70.5 \(\pm\) 0.32 | 65.1 \(\pm\) 0.20 | 66.2 \(\pm\) 0.15 | 46.8 \(\pm\) 0.18 | 29.4 \(\pm\) 0.28 | 74.6 \(\pm\) 0.06 |
| Â | EGAAC | 70.5 \(\pm\) 0.71 | 60.9 \(\pm\) 0.54 | 62.9 \(\pm\) 0.29 | 44.4 \(\pm\) 0.10 | 25.6 \(\pm\) 0.17 | 71.1 \(\pm\) 0.01 |
| Â | AAindex | 74.5 \(\pm\) 0.40 | 60.0 \(\pm\) 043 | 63.0 \(\pm\) 0.27 | 45.9 \(\pm\) 0.11 | 28.2 \(\pm\) 0.17 | 75.2 \(\pm\) 0.10 |
| Â | BLOSUM62 | 70.0 \(\pm\) 0.42 | 66.4 \(\pm\) 0.40 | 67.1 \(\pm\) 0.27 | 47.2 \(\pm\) 0.20 | 30.1 \(\pm\) 0.30 | 75.4 \(\pm\) 0.11 |
AdaBoost | BE | 23.5 \(\pm\) 0.00 | 95.4 \(\pm\) 0.00 | 80.3 \(\pm\) 0.00 | 33.8 \(\pm\) 0.00 | 27.8 \(\pm\) 0.00 | 78.9 \(\pm\) 0.00 |
| Â | AAC | 18.0 \(\pm\) 0.00 | 95.6 \(\pm\) 0.00 | 79.3 \(\pm\) 0.00 | 26.8 \(\pm\) 0.00 | 23.1 \(\pm\) 0.00 | 76.2 \(\pm\) 0.00 |
| Â | EGAAC | 2.60 \(\pm\) 0.00 | 99.4 \(\pm\) 0.00 | 79.0 \(\pm\) 0.00 | 5.00 \(\pm\) 0.00 | 7.90 \(\pm\) 0.00 | 71.5 \(\pm\) 0.00 |
| Â | AAindex | 25.8 \(\pm\) 0.00 | 95.2 \(\pm\) 0.00 | 80.6 \(\pm\) 0.00 | 35.0 \(\pm\) 0.00 | 29.5 \(\pm\) 0.00 | 79.5 \(\pm\) 0.00 |
| Â | BLOSUM62 | 23.1 \(\pm\) 0.00 | 95.3 \(\pm\) 0.00 | 80.1 \(\pm\) 0.00 | 32.9 \(\pm\) 0.00 | 26.9 \(\pm\) 0.00 | 79.0 \(\pm\) 0.00 |
LightGBM | BE | 71.9 \(\pm\) 0.00 | 84.0 \(\pm\) 0.00 | 81.4 \(\pm\) 0.00 | 62.0 \(\pm\) 0.00 | 50.8 \(\pm\) 0.00 | 86.6 \(\pm\) 0.00 |
| Â | AAC | 69.0 \(\pm\) 0.00 | 72.2 \(\pm\) 0.00 | 71.5 \(\pm\) 0.00 | 50.5 \(\pm\) 0.00 | 34.9 \(\pm\) 0.00 | 78.4 \(\pm\) 0.00 |
| Â | EGAAC | 72.4 \(\pm\) 0.00 | 59.0 \(\pm\) 0.00 | 61.9 \(\pm\) 0.00 | 44.4 \(\pm\) 0.00 | 25.7 \(\pm\) 0.00 | 71.1 \(\pm\) 0.00 |
| Â | AAindex | 69.4 \(\pm\) 0.00 | 86.9 \(\pm\) 0.00 | 83.2 \(\pm\) 0.00 | 63.5 \(\pm\) 0.00 | 53.0 \(\pm\) 0.00 | 87.6 \(\pm\) 0.00 |
| Â | BLOSUM62 | 71.7 \(\pm\) 0.00 | 86.2 \(\pm\) 0.00 | 83.2 \(\pm\) 0.00 | 64.2 \(\pm\) 0.00 | 53.8 \(\pm\) 0.00 | 88.1 \(\pm\) 0.00 |
LSTM | BE | 79.7 \(\pm\) 5.22 | 82.2 \(\pm\) 3.29 | 81.7 \(\pm\) 1.54 | 64.7 \(\pm\) 0.66 | 54.9 \(\pm\) 0.60 | 89.0 \(\pm\) 0.14 |
| Â | WE | 75.2 \(\pm\) 1.82 | 83.4 \(\pm\) 1.32 | 81.7 \(\pm\) 0.62 | 63.3 \(\pm\) 0.40 | 52.7 \(\pm\) 0.51 | 87.5 \(\pm\) 0.21 |
| Â | AAindex | 79.0 \(\pm\) 4.48 | 82.5 \(\pm\) 3.21 | 81.7 \(\pm\) 1.61 | 64.6 \(\pm\) 0.77 | 54.6 \(\pm\) 0.72 | 88.7 \(\pm\) 0.32 |
| Â | BLOSUM62 | 75.5 \(\pm\) 4.72 | 83.8 \(\pm\) 2.88 | 82.0 \(\pm\) 1.33 | 63.9 \(\pm\) 0.68 | 53.6 \(\pm\) 0.82 | 88.5 \(\pm\) 0.43 |
BiLSTM | BE | 75.8 \(\pm\) 3.49 | 84.3 \(\pm\) 1.77 | 82.5 \(\pm\) 0.71 | 64.6 \(\pm\) 0.50 | 54.5 \(\pm\) 0.67 | 88.9 \(\pm\) 0.25 |
| Â | WE | 77.5 \(\pm\) 2.79 | 81.0 \(\pm\) 0.20 | 80.3 \(\pm\) 1.03 | 62.3 \(\pm\) 0.60 | 51.5 \(\pm\) 0.73 | 87.4 \(\pm\) 0.28 |
| Â | AAindex | 79.3 \(\pm\) 3.45 | 82.2 \(\pm\) 2.59 | 81.6 \(\pm\) 1.37 | 64.5 \(\pm\) 0.88 | 54.5 \(\pm\) 0.96 | 88.9 \(\pm\) 0.26 |
| Â | BLOSUM62 | 75.5 \(\pm\) 7.16 | 83.5 \(\pm\) 4.16 | 81.8 \(\pm\) 1.81 | 63.7 \(\pm\) 0.58 | 53.5 \(\pm\) 0.50 | 88.7 \(\pm\) 0.13 |
CNN | BE | 82.1 \(\pm\) 1.08 | 82.2 \(\pm\) 0.80 | 82.1 \(\pm\) 0.43 | 66.0 \(\pm\) 0.33 | 56.5 \(\pm\) 0.38 | 89.6 \(\pm\) 0.07 |
| Â | WE | 79.0 \(\pm\) 2.13 | 83.4 \(\pm\) 1.33 | 82.4 \(\pm\) 0.54 | 65.4 \(\pm\) 0.48 | 55.6 \(\pm\) 0.63 | 89.1 \(\pm\) 0.16 |
| Â | AAindex | 82.1 \(\pm\) 3.27 | 81.2 \(\pm\) 2.06 | 81.4 \(\pm\) 0.96 | 65.0 \(\pm\) 0.39 | 55.3 \(\pm\) 0.38 | 89.1 \(\pm\) 0.14 |
| Â | BLOSUM62 | 79.2 \(\pm\) 4.92 | 83.1 \(\pm\) 2.88 | 82.3 \(\pm\) 1.26 | 65.3 \(\pm\) 0.43 | 55.6 \(\pm\) 0.38 | 89.4 \(\pm\) 0.11 |
PlantNh-Kcr | BE | 81.1 \(\pm\) 3.23 | 83.3 \(\pm\) 2.09 | 82.8 \(\pm\) 0.99 | 66.5 \(\pm\) 0.50 | 57.2 \(\pm\) 0.50 | 89.9 \(\pm\) 0.19 |