Table 3 Average classification accuracies for 13 numerical representations. Averages over the six classifiers are in bold
DataSet/ | Numerical representation | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
classification model | Integer | Integer (Other) | Real | Atomic | EIIP | PP | Paired Num. | NN based doublet | Codon | Just-A | Just-C | Just-G | Just-T |
Primates (148 sequences) | |||||||||||||
Linear Discriminant | 97.3% | 98.0% | 99.3% | 98.6% | 99.3% | 99.3% | 97.3% | 97.3% | 98.0% | 98.0% | 97.3% | 96.6% | 96.6% |
Linear SVM | 97.3% | 95.9% | 98.6% | 96.6% | 97.3% | 98.0% | 95.9% | 97.3% | 94.6% | 98.0% | 96.6% | 96.6% | 95.3% |
Quadratic SVM | 97.3% | 95.9% | 98.6% | 93.2% | 95.9% | 98.6% | 96.6% | 98.6% | 95.9% | 98.0% | 98.0% | 97.3% | 95.9% |
Fine KNN | 98.0% | 98.0% | 100.0% | 98.0% | 96.6% | 100.0% | 99.3% | 99.3% | 98.0% | 100.0% | 98.6% | 100.0% | 98.6% |
Subspace Discriminant | 98.0% | 97.3% | 99.3% | 98.0% | 99.3% | 98.6% | 95.3% | 97.3% | 95.9% | 98.0% | 97.3% | 98.0% | 95.3% |
Subspace KNN | 98.0% | 97.3% | 98.6% | 96.6% | 95.9% | 98.0% | 100% | 98.0% | 98.0% | 99.3% | 97.3% | 98.6% | 98.6% |
Average | 97.7% | 97.1% | 99.1% | 96.8% | 97.4% | 98.8% | 97.4% | 98.0% | 96.7% | 98.6% | 97.5% | 97.9% | 96.7% |
Protists (159 sequences) | |||||||||||||
Linear Discriminant | 83.6% | 84.9% | 85.5% | 86.2% | 86.2% | 84.3% | 85.5% | 83.0% | 85.5% | 84.3% | 83.6% | 83.0% | 83.6% |
Linear SVM | 84.3% | 83.0% | 83.6% | 83.0% | 83.0% | 71.7% | 82.4% | 83.0% | 83.6% | 83.6% | 83.6% | 83.6% | 83.0% |
Quadratic SVM | 84.9% | 84.9% | 83.6% | 82.4% | 83.0% | 81.1% | 85.5% | 84.9% | 86.2% | 83.0% | 84.3% | 83.0% | 86.2% |
Fine KNN | 86.8% | 86.2% | 81.8% | 84.3% | 88.1% | 78.0% | 89.9% | 88.7% | 91.8% | 86.8% | 88.7% | 93.7% | 92.5% |
Subspace Discriminant | 85.5% | 84.9% | 88.1% | 86.8% | 85.5% | 86.8% | 83.6% | 83.0% | 85.5% | 84.9% | 83.6% | 83.0% | 83.6% |
Subspace KNN | 88.7% | 87.4% | 91.8% | 85.5% | 88.1% | 91.2% | 89.9% | 88.1% | 93.1% | 86.8% | 88.1% | 92.5% | 93.7% |
Average | 85.6% | 85.2% | 85.7% | 84.7% | 85.7% | 82.2% | 86.1% | 85.1% | 87.6% | 84.9% | 85.3% | 86.5% | 87.1% |
Fungi (226 sequences) | |||||||||||||
Linear Discriminant | 76.3% | 76.8% | 82.1% | 50.9% | 57.1% | 80.4% | 75.4% | 68.8% | 77.7% | 81.7% | 70.5% | 71.9% | 79.0% |
Linear SVM | 66.5% | 58.0% | 76.8% | 49.1% | 46.0% | 73.7% | 73.2% | 66.1% | 71.0% | 75.9% | 64.7% | 66.1% | 75.4% |
Quadratic SVM | 58.9% | 59.8% | 82.6% | 33.9% | 37.9% | 79.9% | 71.4% | 67.4% | 63.4% | 71.0% | 67.9% | 71.4% | 64.3% |
Fine KNN | 61.6% | 56.7% | 84.4% | 49.6% | 54.9% | 85.7% | 72.3% | 65.2% | 58.0% | 68.8% | 61.6% | 68.8% | 67.9% |
Subspace Discriminant | 74.6% | 75.0% | 78.6% | 46.0% | 55.4% | 79.0% | 75.0% | 71.4% | 78.1% | 79.9% | 68.8% | 69.2% | 78.6% |
Subspace KNN | 63.4% | 58.9% | 89.3% | 51.8% | 58.0% | 89.3% | 68.3% | 63.8% | 59.8% | 67.9% | 65.6% | 72.8% | 64.3% |
Average | 66.9% | 64.2% | 82.3% | 46.9% | 51.6% | 81.3% | 72.6% | 67.1% | 68.0% | 74.2% | 66.5% | 70.0% | 71.6% |
Plants (174 sequences) | |||||||||||||
Linear Discriminant | 96.0% | 95.4% | 76.4% | 92.5% | 93.7% | 91.4% | 95.4% | 96.0% | 95.4% | 96.0% | 96.0% | 96.0% | 96.0% |
Linear SVM | 96.0% | 96.0% | 85.6% | 96.0% | 96.0% | 87.9% | 94.8% | 96.0% | 96.0% | 96.0% | 96.0% | 96.0% | 96.0% |
Quadratic SVM | 96.0% | 96.0% | 86.8% | 96.0% | 96.0% | 88.5% | 94.3% | 96.0% | 96.0% | 96.0% | 96.0% | 96.0% | 96.0% |
Fine KNN | 93.1% | 94.8% | 91.4% | 94.3% | 94.3% | 90.8% | 86.8% | 93.1% | 94.3% | 93.7% | 91.4% | 93.1% | 93.1% |
Subspace Discriminant | 96.0% | 95.4% | 87.4% | 94.8% | 95.4% | 87.9% | 94.8% | 96.0% | 96.0% | 96.0% | 96.0% | 96.0% | 96.0% |
Subspace KNN | 93.7% | 94.3% | 90.2% | 94.3% | 94.3% | 90.2% | 92.5% | 92.5% | 94.8% | 93.7% | 94.3% | 94.8% | 94.3% |
Average | 95.1% | 95.3% | 86.3% | 94.7% | 95.0% | 89.5% | 93.1% | 94.9% | 95.4% | 95.2% | 95.0% | 95.3% | 95.2% |
Amphibians (290 sequences) | |||||||||||||
Linear Discriminant | 92.1% | 91.4% | 95.5% | 89.0% | 89.3% | 99.0% | 94.5% | 93.4% | 91.4% | 96.2% | 93.4% | 93.8% | 91.7% |
Linear SVM | 91.0% | 90.0% | 89.0% | 88.3% | 88.6% | 93.1% | 89.0% | 91.4% | 90.0% | 93.1% | 92.1% | 92.4% | 90.3% |
Quadratic SVM | 90.3% | 89.0% | 92.4% | 59.3% | 83.4% | 96.6% | 91.0% | 93.1% | 86.9% | 94.1% | 93.1% | 93.4% | 90.7% |
Fine KNN | 90.0% | 86.9% | 96.6% | 83.8% | 83.4% | 98.3% | 87.9% | 92.1% | 89.7% | 93.4% | 91.7% | 94.8% | 89.7% |
Subspace Discriminant | 90.7% | 90.3% | 90.0% | 89.3% | 89.3% | 96.6% | 90.3% | 91.7% | 90.3% | 95.2% | 92.8% | 92.1% | 91.0% |
Subspace KNN | 88.3% | 86.6% | 94.1% | 85.2% | 84.5% | 98.3% | 89.7% | 92.8% | 87.2% | 94.5% | 90.0% | 94.8% | 90.3% |
Average | 90.4% | 89.0% | 92.9% | 82.5% | 86.4% | 97.0% | 90.4% | 92.4% | 89.3% | 94.4% | 92.2% | 93.6% | 90.6% |
Mammals (830 sequences) | |||||||||||||
Linear Discriminant | 98.3% | 97.6% | 97.7% | 97.0% | 96.0% | 97.1% | 96.6% | 97.2% | 96.7% | 98.0% | 96.9% | 96.3% | 96.3% |
Linear SVM | 90.6% | 89.6% | 88.9% | 84.5% | 85.3% | 91.6% | 86.5% | 91.2% | 88.8% | 90.8% | 90.0% | 88.2% | 88.1% |
Quadratic SVM | 92.4% | 89.9% | 91.0% | 32.9% | 41.7% | 93.4% | 88.0% | 93.4% | 89.9% | 90.7% | 92.5% | 89.8% | 90.5% |
Fine KNN | 94.1% | 92.3% | 96.0% | 79.9% | 81.0% | 96.6% | 93.9% | 93.7% | 91.7% | 96.3% | 96.3% | 94.8% | 95.5% |
Subspace Discriminant | 92.3% | 91.9% | 92.3% | 88.3% | 87.7% | 94.0% | 90.2% | 91.7% | 90.4% | 92.3% | 93.4% | 91.9% | 91.3% |
Subspace KNN | 92.8% | 90.8% | 95.5% | 78.2% | 79.2% | 96.4% | 91.2% | 93.3% | 89.2% | 94.8% | 94.3% | 94.9% | 92.2% |
Average | 93.4% | 92.0% | 93.6% | 76.8% | 78.5% | 94.9% | 91.1% | 93.4% | 91.1% | 93.8% | 93.9% | 92.7% | 92.3% |
Insects (898 sequences) | |||||||||||||
Linear Discriminant | 92.2% | 92.7% | 90.1% | 91.6% | 92.2% | 94.2% | 93.3% | 92.4% | 89.2% | 93.1% | 92.1% | 94.4% | 90.4% |
Linear SVM | 86.9% | 82.6% | 85.9% | 66.7% | 69.5% | 85.3% | 86.4% | 90.0% | 80.5% | 89.4% | 87.4% | 88.4% | 86.2% |
Quadratic SVM | 85.0% | 81.8% | 86.7% | 24.4% | 21.3% | 87.1% | 85.7% | 89.6% | 82.6% | 89.5% | 88.0% | 89.6% | 85.3% |
Fine KNN | 82.0% | 79.3% | 80.0% | 62.5% | 68.0% | 93.2% | 83.3% | 87.9% | 80.8% | 85.6% | 83.6% | 87.9% | 83.0% |
Subspace Discriminant | 85.7% | 83.9% | 88.3% | 77.5% | 79.3% | 89.1% | 88.0% | 88.2% | 82.1% | 87.1% | 87.6% | 88.2% | 86.4% |
Subspace KNN | 80.4% | 77.3% | 90.5% | 61.0% | 67.6% | 92.0% | 81.4% | 86.9% | 77.4% | 85.4% | 86.0% | 89.3% | 81.4% |
Average | 85.4% | 82.9% | 86.9% | 64.0% | 66.3% | 90.2% | 86.4% | 89.2% | 82.1% | 88.4% | 87.5% | 89.6% | 85.5% |
3Classes (2170 sequences; Subspace Discriminant & Subspace KNN omitted) | |||||||||||||
Linear Discriminant | 99.9% | 99.9% | 99.6% | 99.4% | 99.7% | 99.7% | 99.7% | 99.7% | 99.8% | 99.8% | 99.9% | 99.9% | 99.6% |
Linear SVM | 94.1% | 90.2% | 99.4% | 89.8% | 89.3% | 99.6% | 99.2% | 98.1% | 94.6% | 99.1% | 97.3% | 99.3% | 97.9% |
Quadratic SVM | 97.5% | 92.5% | 99.4% | 66.6% | 78.8% | 99.7% | 99.5% | 98.7% | 97.6% | 99.4% | 98.4% | 99.5% | 98.8% |
Fine KNN | 95.9% | 95.2% | 97.6% | 93.3% | 94.4% | 95.9% | 97.6% | 97.7% | 96.4% | 98.9% | 98.0% | 99.2% | 98.4% |
Average | 96.9% | 94.5% | 99.0% | 87.3% | 90.6% | 98.7% | 99.0% | 98.6% | 97.1% | 99.3% | 98.4% | 99.5% | 98.7% |
Vertebrates (4322 sequences; Subspace Discriminant & Subspace KNN omitted) | |||||||||||||
Linear Discriminant | 99.7% | 99.7% | 99.6% | 99.3% | 99.5% | 99.7% | 99.2% | 99.3% | 99.3% | 99.3% | 99.4% | 99.5% | 99.2% |
Linear SVM | 98.3% | 98.2% | 98.5% | 96.3% | 96.8% | 97.9% | 98.0% | 98.4% | 98.2% | 98.2% | 98.5% | 98.8% | 98.4% |
Quadratic SVM | 98.1% | 96.6% | 99.0% | 40.6% | 34.0% | 98.7% | 98.4% | 98.2% | 96.7% | 98.5% | 98.7% | 98.8% | 98.6% |
Fine KNN | 97.1% | 96.1% | 98.4% | 88.3% | 91.7% | 97.9% | 96.4% | 96.3% | 95.3% | 96.4% | 97.5% | 97.6% | 97.2% |
Average | 98.3% | 97.7% | 98.9% | 81.1% | 80.5% | 98.6% | 98.0% | 98.1% | 97.4% | 98.1% | 98.5% | 98.7% | 98.4% |
Table average | 90.0% | 88.7% | 91.6% | 79.4% | 81.3% | 92.3% | 90.5% | 90.7% | 89.4% | 91.9% | 90.5% | 91.5% | 90.7% |