Skip to main content

Table 5 The comparison of the performance of the four clustering algorithms over different matrix transformation methods by various indices (Dunn, Davies–Bouldin, eta-squared and omega-squared) and correlations between MSt and MSb of clusters

From: The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix

Transformation methods Clustering algo. Dunn mean (SD) Davies-Bouldin mean (SD) Eta-squared mean (SD) Omega-squared mean (SD) Cor (MSt, MSb)
Lower triangle RCKmeans 0.2 (0.24) 8.06 (4.55) 0.32 (0.18) 0.28 (0.16) 0.82
RCDTC 0.23 (0.24) 6.73 (3.63) 0.4 (0.14) 0.35 (0.14) 0.9
RCPCA 0.18 (0.15) 7.22 (4.53) 0.45 (0.09) 0.33 (0.12) 0.83
RCPCA_RBF 0.14 (0.12) 8.84 (5.33) 0.32 (0.11) 0.26 (0.12) 0.78
Upper triangle RCKmeans 0.17 (0.29) 8.06 (4.55) 0.32 (0.18) 0.27 (0.17) 0.82
RCDTC 0.21 (0.24) 6.58 (3.2) 0.39 (0.14) 0.34 (0.15) 0.89
RCPCA 0.18 (0.18) 7.02 (3.46) 0.45 (0.08) 0.34 (0.11) 0.82
RCPCA_RBF 0.14 (0.14) 8.66 (5.02) 0.33 (0.1) 0.26 (0.11) 0.78
Average RCKmeans 0.2 (0.22) 8.31 (5.32) 0.34 (0.18) 0.29 (0.16) 0.82
RCDTC 0.23 (0.24) 6.61 (3.26) 0.41 (0.14) 0.35 (0.15) 0.87
RCPCA 0.17 (0.13) 7.24 (4.02) 0.44 (0.09) 0.33 (0.12) 0.81
RCPCA_RBF 0.14 (0.12) 8.54 (4.64) 0.33 (0.11) 0.27 (0.11) 0.78
Reciprocal RCKmeans 0.21 (0.24) 7.5 (3.57) 0.33 (0.18) 0.29 (0.17) 0.82
RCDTC 0.22 (0.24) 6.8 (3.51) 0.4 (0.14) 0.35 (0.15) 0.91
RCPCA 0.17 (0.13) 6.83 (3.8) 0.45 (0.08) 0.34 (0.11) 0.82
RCPCA_RBF 0.14 (0.11) 8.74 (5.07) 0.32 (0.11) 0.26 (0.11) 0.79
Non-reciprocal RCKmeans 0.2 (0.22) 7.8 (4.05) 0.33 (0.17) 0.29 (0.16) 0.81
RCDTC 0.23 (0.24) 6.68 (3.29) 0.4 (0.14) 0.35 (0.15) 0.91
RCPCA 0.19 (0.15) 6.87 (3.57) 0.46 (0.07) 0.35 (0.11) 0.81
RCPCA_RBF 0.14 (0.12) 8.96 (5.22) 0.32 (0.11) 0.26 (0.12) 0.78