Table 7 Feature importance calculated for the highest quality Spark supervised algorithms (Decision Trees (DT) and Random Forest (RF)). The entropy, the number of nodes that included certain features in the Random Forest building with RUS pre-processing and the average impurity decrease of the MLlib 2.0 Random Forest with ROS variants are presented for the alignment-based, alignment-free and alignment-based + alignment-free feature combinations The Random Oversampling pre-processing (ROS) is accompanied by the corresponding resampling size value
RUS + DT-Spark Weka | RUS + RF-Spark/Gini Weka | RF MLlib 2.0-Spark/Gini (Avg. Impurity Decrease) | |||||
|---|---|---|---|---|---|---|---|
Entropy | Avg. Impurity Decrease | Number of Nodes | Normal | ROS-100 | ROS-130 | RUS | |
Alignment-based Features/Algorithm | |||||||
nw | 0.789 | 0.520 | 42 | 0.809 | 0.180 | 0.175 | 0.171 |
sw | 0.982 | 0.360 | 802 | 0.035 | 0.642 | 0.647 | 0.647 |
profile3 | 0.783 | 0.360 | 417 | 0.043 | 0.167 | 0.167 | 0.167 |
profile5 | 0.732 | 0.290 | 235 | 0.033 | 0.004 | 0.001 | 0.007 |
profile7 | 0.712 | 0.240 | 330 | 0.080 | 0.008 | 0.010 | 0.008 |
Alignment-free Features | |||||||
aac | 0.624 | 0.400 | 1891 | 0.033 | 0.173 | 0.171 | 0.169 |
Auto_Geary | 0.000 | 0.310 | 64 | 0.000 | 0.000 | 0.000 | 0.000 |
Auto_Moran | 0.000 | 0.320 | 75 | 0.000 | 0.000 | 0.000 | 0.000 |
Auto_Total | 0.000 | 0.370 | 1124 | 0.000 | 0.000 | 0.000 | 0.001 |
CTD | 0.408 | 0.310 | 1012 | 0.070 | 0.134 | 0.133 | 0.137 |
CTD_C | 0.566 | 0.300 | 1482 | 0.071 | 0.060 | 0.062 | 0.066 |
CTD_D | 0.407 | 0.320 | 1239 | 0.074 | 0.030 | 0.029 | 0.033 |
CTD_T | 0.529 | 0.290 | 1385 | 0.076 | 0.028 | 0.035 | 0.036 |
fcm | 0.265 | 0.310 | 1010 | 0.012 | 0.004 | 0.021 | 0.021 |
2-mers | 0.158 | 0.390 | 954 | 0.022 | 0.003 | 0.003 | 0.002 |
2-mers_don’t care ps-1 | 0.000 | 0.320 | 847 | 0.000 | 0.000 | 0.000 | 0.000 |
2-mers_ don’t care ps-2 | 0.000 | 0.310 | 768 | 0.001 | 0.000 | 0.000 | 0.000 |
2-mers_ don’t care ps-3 | 0.000 | 0.260 | 772 | 0.000 | 0.000 | 0.000 | 0.001 |
3-mers | 0.078 | 0.370 | 1523 | 0.064 | 0.006 | 0.005 | 0.006 |
3-mers_ don’t care ps-1 | 0.000 | 0.290 | 600 | 0.001 | 0.000 | 0.000 | 0.001 |
3-mers_ don’t care ps-2 | 0.000 | 0.270 | 653 | 0.001 | 0.000 | 0.000 | 0.001 |
3-mers_ don’t care ps-3 | 0.000 | 0.270 | 602 | 0.002 | 0.000 | 0.000 | 0.001 |
length | 0.507 | 0.400 | 2890 | 0.353 | 0.166 | 0.165 | 0.154 |
nandy | 0.109 | 0.260 | 902 | 0.009 | 0.000 | 0.000 | 0.001 |
pseaa10 | 0.000 | 0.240 | 825 | 0.000 | 0.000 | 0.000 | 0.001 |
pseaa3 | 0.611 | 0.380 | 1397 | 0.022 | 0.205 | 0.202 | 0.166 |
pseaa4 | 0.609 | 0.380 | 1652 | 0.112 | 0.155 | 0.156 | 0.184 |
QSO_maxlag_30_weight_01 | 0.280 | 0.240 | 1054 | 0.075 | 0.035 | 0.018 | 0.020 |
QSOCN_maxlag_30 | 0 | 0.250 | 513 | 0.001 | 0.000 | 0.000 | 0.001 |
Alignment-based + Alignment-free Features/Algorithm | |||||||
nw | 0.789 | 0.280 | 131 | 0.786 | 0.382 | 0.373 | 0.374 |
sw | 0.987 | 0.470 | 646 | 0.005 | 0.135 | 0.139 | 0.126 |
profile3 | 0.769 | 0.280 | 271 | 0.005 | 0.098 | 0.101 | 0.097 |
profile5 | 0.727 | 0.290 | 230 | 0.016 | 0.168 | 0.168 | 0.137 |
profile7 | 0.710 | 0.260 | 229 | 0.004 | 0.083 | 0.084 | 0.126 |
aac | 0.623 | 0.190 | 230 | 0.015 | 0.073 | 0.071 | 0.072 |
Auto_Geary | 0.000 | 0.300 | 11 | 0.000 | 0.000 | 0.000 | 0.000 |
Auto_Moran | 0.000 | 0.270 | 11 | 0.000 | 0.000 | 0.000 | 0.000 |
Auto_Total | 0.000 | 0.510 | 147 | 0.001 | 0.000 | 0.000 | 0.000 |
CTD | 0.411 | 0.360 | 109 | 0.005 | 0.000 | 0.000 | 0.000 |
CTD_C | 0.570 | 0.340 | 204 | 0.039 | 0.032 | 0.032 | 0.032 |
CTD_D | 0.411 | 0.390 | 151 | 0.009 | 0.002 | 0.001 | 0.001 |
CTD_T | 0.531 | 0.320 | 164 | 0.001 | 0.002 | 0.003 | 0.004 |
fcm | 0.260 | 0.300 | 154 | 0.005 | 0.000 | 0.000 | 0.001 |
2-mers | 0.155 | 0.200 | 81 | 0.003 | 0.000 | 0.000 | 0.000 |
2-mers_don’t care ps-1 | 0.000 | 0.410 | 104 | 0.000 | 0.000 | 0.000 | 0.000 |
2-mers_ don’t care ps-2 | 0.000 | 0.410 | 98 | 0.000 | 0.000 | 0.000 | 0.000 |
2-mers_ don’t care ps-3 | 0.000 | 0.400 | 82 | 0.001 | 0.000 | 0.000 | 0.000 |
3-mers | 0.074 | 0.230 | 97 | 0.010 | 0.000 | 0.000 | 0.000 |
3-mers_ don’t care ps-1 | 0.000 | 0.390 | 69 | 0.000 | 0.000 | 0.000 | 0.000 |
3-mers_ don’t care ps-2 | 0.000 | 0.340 | 49 | 0.001 | 0.000 | 0.000 | 0.000 |
3-mers_ don’t care ps-3 | 0.000 | 0.390 | 59 | 0.001 | 0.000 | 0.000 | 0.000 |
length | 0.504 | 0.230 | 231 | 0.059 | 0.012 | 0.014 | 0.014 |
nandy | 0.113 | 0.320 | 101 | 0.001 | 0.000 | 0.000 | 0.001 |
pseaa10 | 0.000 | 0.310 | 97 | 0.001 | 0.000 | 0.000 | 0.000 |
pseaa3 | 0.613 | 0.190 | 142 | 0.009 | 0.006 | 0.007 | 0.004 |
pseaa4 | 0.610 | 0.210 | 147 | 0.001 | 0.005 | 0.005 | 0.009 |
QSO_maxlag_30_weight = 0.1 | 0.286 | 0.270 | 108 | 0.020 | 0.001 | 0.001 | 0.000 |
QSO_maxlag_30 | 0.000 | 0.340 | 47 | 0.000 | 0.000 | 0.000 | 0.000 |