Table 1 Simulation results under different model assumptions. In each cell, median (MAD) is based on 100 replicates, and P-value is computed from the Wilcoxon test for the proposed method and each competing method
Method | ARI | Recall | Precision | F1 | ||||
|---|---|---|---|---|---|---|---|---|
Median (MAD) | P-value | Median (MAD) | P-value | Median (MAD) | P-value | Median (MAD) | P-value | |
 snbClust |  | |||||||
Proposed | 0.564 (0.123) | - | 0.940 (0.040) | - | 0.430 (0.026) | - | 0.575 (0.027) | - |
CIDR | 0.128 (0.065) | 0.000 | -Â - | - | -Â - | - | -Â - | - |
SC3 | 0.288 (0.102) | 0.000 | -Â - | - | -Â - | - | -Â - | - |
Seurat | 0.462 (0.050) | 0.000 | -Â - | - | -Â - | - | -Â - | - |
scDeepCluster | 0.472 (0.056) | 0.002 | -Â - | - | -Â - | - | -Â - | - |
RZiMM | 0.464 (0.404) | 0.099 | 0.890 (0.070) | 0.000 | 0.250 (0.220) | 0.012 | 0.547 (0.093) | 0.027 |
snbClust | 0.627 (0.268) | 0.946 | 0.980 (0.020) | 0.915 | 0.268 (0.137) | 0.000 | 0.391 (0.175) | 0.000 |
sparseKmeans | 0.001 (0.002) | 0.000 | 1.000 (0.000) | 1.000 | 0.050 (0.000) | 0.000 | 0.095 (0.000) | 0.000 |
M3Drop | -Â - | - | 0.290 (0.030) | 0.000 | 0.100 (0.012) | 0.000 | 0.148 (0.017) | 0.000 |
NBDrop | -Â - | - | 0.280 (0.040) | 0.000 | 0.104 (0.014) | 0.000 | 0.152 (0.020) | 0.000 |
 RZiMM |  | |||||||
Proposed | 0.897 (0.103) | - | 1.000 (0.000) | - | 0.573 (0.080) | - | 0.712 (0.060) | - |
CIDR | 0.008 (0.007) | 0.000 | -Â - | - | -Â - | - | -Â - | - |
SC3 | 0.000 (0.001) | 0.000 | -Â - | - | -Â - | - | -Â - | - |
Seurat | 0.034 (0.029) | 0.000 | -Â - | - | -Â - | - | -Â - | - |
scDeepCluster | 0.014(0.014) | 0.000 | -Â - | - | -Â - | - | -Â - | - |
MNN-Graph | 0.001 (0.001) | 0.000 | -Â - | - | -Â - | - | -Â - | - |
MNN-Kmeans | 0.002 (0.001) | 0.000 | -Â - | - | -Â - | - | -Â - | - |
RZiMM | 1.000 (0.000) | 0.999 | 1.000 (0.000) | 0.041 | 0.883 (0.000) | 1.000 | 0.909 (0.000) | 1.000 |
snbClust | − 0.001 (0.001) | 0.000 | 0.165 (0.165) | 0.000 | 0.055 (0.005) | 0.000 | 0.097 (0.010) | 0.000 |
sparseKmeans | 0.069 (0.012) | 0.000 | 0.405 (0.385) | 0.000 | 0.631 (0.369) | 0.729 | 0.179 (0.031) | 0.000 |
M3Drop | -Â - | - | 0.695 (0.025) | 0.000 | 0.188 (0.007) | 0.000 | 0.297 (0.012) | 0.000 |
NBDrop | -Â - | - | 1.000 (0.000) | 1.000 | 0.100 (0.000) | 0.000 | 0.182 (0.000) | 0.000 |
 CIDR |  | |||||||
Proposed | 0.965 (0.035) | - | 0.990 (0.010) | - | 0.718 (0.036) | - | 0.820 (0.017) | - |
CIDR | 0.999 (0.001) | 0.994 | -Â - | - | -Â - | - | -Â - | - |
SC3 | 1.000 (0.000) | 1.000 | -Â - | - | -Â - | - | -Â - | - |
Seurat | 1.000 (0.000) | 1.000 | -Â - | - | -Â - | - | -Â - | - |
scDeepCluster | 0.570 (0.138) | 0.000 | -Â - | - | -Â - | - | -Â - | - |
RZiMM | 0.957 (0.043) | 0.015 | 0.880 (0.040) | 0.000 | 0.587 (0.027) | 0.000 | 0.704 (0.032) | 0.000 |
snbClust | 0.954 (0.046) | 0.028 | 0.955 (0.015) | 0.000 | 0.977 (0.010) | 1.000 | 0.964 (0.006) | 1.000 |
sparseKmeans | 0.913 (0.041) | 0.000 | 0.915 (0.085) | 0.001 | 0.192 (0.092) | 0.000 | 0.193 (0.000) | 0.000 |
M3Drop | -Â - | - | 0.810 (0.020) | 0.000 | 0.147 (0.004) | 0.000 | 0.248 (0.007) | 0.000 |
NBDrop | -Â - | - | 0.990 (0.010) | 0.139 | 0.109 (0.001) | 0.000 | 0.196 (0.001) | 0.000 |