Table 2 Comparison of the classification performance obtained by Random Forest. For three clustering strategies, we compare 4 different imputation methods: halfMin, kNN3, EM, and SVD. And four feature selection methods: Fisher, Gini, T-test and Stability. These are described in the Methods. The method used for subsequent pathway analysis is in bold
From: Metabolomic biosignature differentiates melancholic depressive patients from healthy controls
Imputation | halfMin | kNN3 | EM | SVD | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
FS method | Fisher | Gini | T-test | Stability | Fisher | Gini | T-test | Stability | Fisher | Gini | T-test | Stability | Fisher | Gini | T-test | Stability |
Raw Features | ||||||||||||||||
Accuracy | 80.42 % | 80.36 % | 80.42 % | 80.34 % | 78.68 % | 80.43 % | 77.84 % | 83.84 % | 77.84 % | 76.87 % | 77.84 % | 78.74 % | 77.84 % | 76.11 % | 77.84 % | 81.18 % |
Sensitivity | 73.33 % | 76.67 % | 73.33 % | 76.67 % | 73.33 % | 76.67 % | 73.33 % | 76.67 % | 73.33 % | 71.67 % | 73.33 % | 68.33 % | 73.33 % | 66.67 % | 73.33 % | 76.67 % |
Specificity | 82.22 % | 81.22 % | 82.22 % | 81.11 % | 80.22 % | 81.33 % | 79.11 % | 85.44 % | 79.11 % | 78.00 % | 79.11 % | 81.11 % | 79.11 % | 78.11 % | 79.11 % | 82.11 % |
Cluster-Representatives (K-means) | ||||||||||||||||
Accuracy | 77.92 % | 80.50 % | 77.92 % | 79.51 % | 78.69 % | 79.74 % | 78.69 % | 79.52 % | 77.07 % | 77.16 % | 75.34 % | 74.15 % | 78.74 % | 78.74 % | 80.48 % | 79.73 % |
Sensitivity | 83.33 % | 88.33 % | 83.33 % | 86.67 % | 76.67 % | 81.67 % | 81.67 % | 81.67 % | 78.33 % | 78.33 % | 78.33 % | 75.00 % | 78.33 % | 78.33 % | 73.33 % | 78.33 % |
Specificity | 77.22 % | 79.22 % | 77.22 % | 78.11 % | 79.33 % | 79.44 % | 78.22 % | 79.22 % | 77.11 % | 77.22 % | 75.11 % | 74.33 % | 79.11 % | 79.11 % | 82.33 % | 80.33 % |
Cluster-Representatives (Hierarchical Clustering) | ||||||||||||||||
Accuracy | 78.06 % | 75.48 % | 78.06 % | 77.01 % | 79.59 % | 79.66 % | 80.50 % | 77.24 % | 73.79 % | 73.79 % | 73.73 % | 69.62 % | 75.47 % | 74.64 % | 76.38 % | 70.38 % |
Sensitivity | 73.33 % | 78.33 % | 73.33 % | 83.33 % | 78.33 % | 83.33 % | 78.33 % | 78.33 % | 73.33 % | 80.00 % | 73.33 % | 70.00 % | 70.00 % | 70.00 % | 70.00 % | 70.00 % |
Specificity | 79.33 % | 75.22 % | 79.33 % | 76.00 % | 80.11 % | 79.22 % | 81.22 % | 77.33 % | 74.00 % | 72.89 % | 74.00 % | 69.89 % | 77.11 % | 76.11 % | 78.22 % | 70.89 % |