Table 3 Summary of external evaluations for unsupervised methods
From: A comparison framework and guideline of clustering methods for mass cytometry data
Datasets | Methods | External evaluations | |||
|---|---|---|---|---|---|
Accuracy | F-measure | NMI | ARI | ||
Cell Cycle | Accense | 0.3529 ± 0.0471 | 0.3500 ± 0.0636 | 0.2490 ± 0.0240 | 0.1682 ± 0.0395 |
PhenoGraph | 0.2309 ± 0.0268 | 0.2789 ± 0.0196 | 0.1364 ± 0.0087 | 0.0683 ± 0.0074 | |
Xshift | 0.3622 ± 0.0419 | 0.3970 ± 0.0383 | 0.1710 ± 0.0165 | 0.0752 ± 0.0353 | |
kmeans | 0.3969 ± 0.0021 | 0.4224 ± 0.0019 | 0.0963 ± 0.0016 | 0.0681 ± 0.0016 | |
flowMeans | 0.3055 ± 0.0061 | 0.3506 ± 0.0051 | 0.1849 ± 0.0047 | 0.0694 ± 0.0058 | |
FlowSOM | 0.6605 ± 0.0021 | 0.6897 ± 0.0029 | 0.1040 ± 0.0035 | 0.1171 ± 0.0025 | |
DEPECHE | 0.2808 ± 0.0126 | 0.3551 ± 0.0110 | 0.1361 ± 0.0246 | 0.0546 ± 0.0197 | |
Colon | Accense | 0.3209 ± 0.0353 | 0.3495 ± 0.0442 | 0.4504 ± 0.0286 | 0.2304 ± 0.0304 |
PhenoGraph | 0.3772 ± 0.0201 | 0.3994 ± 0.0137 | 0.4254 ± 0.0073 | 0.2696 ± 0.0094 | |
Xshift | 0.3187 ± 0.0167 | 0.3094 ± 0.0124 | 0.3763 ± 0.0076 | 0.2399 ± 0.0299 | |
kmeans | 0.4480 ± 0.0216 | 0.4951 ± 0.0086 | 0.4688 ± 0.0073 | 0.3235 ± 0.0132 | |
flowMeans | 0.5095 ± 0.0894 | 0.5901 ± 0.0582 | 0.4705 ± 0.0619 | 0.3724 ± 0.1125 | |
FlowSOM | 0.5597 ± 0.0284 | 0.5888 ± 0.0230 | 0.5303 ± 0.0157 | 0.4157 ± 0.0288 | |
DEPECHE | 0.5902 ± 0.0186 | 0.6898 ± 0.0132 | 0.4694 ± 0.0239 | 0.5042 ± 0.0188 | |
Levine13dim | Accense | 0.6055 ± 0.0946 | 0.6745 ± 0.0929 | 0.7486 ± 0.0603 | 0.6408 ± 0.1034 |
PhenoGraph | 0.8880 ± 0.0015 | 0.9123 ± 0.0167 | 0.8639 ± 0.0078 | 0.8884 ± 0.0159 | |
Xshift | 0.7573 ± 0.0091 | 0.7606 ± 0.0125 | 0.7359 ± 0.0118 | 0.7465 ± 0.0116 | |
kmeans | 0.5684 ± 0.0504 | 0.6293 ± 0.0325 | 0.7070 ± 0.0193 | 0.5721 ± 0.0465 | |
flowMeans | 0.8470 ± 0.0486 | 0.8842 ± 0.0343 | 0.8352 ± 0.0282 | 0.8349 ± 0.0459 | |
FlowSOM | 0.8540 ± 0.0235 | 0.8760 ± 0.0200 | 0.8590 ± 0.0097 | 0.8732 ± 0.0168 | |
DEPECHE | 0.6929 ± 0.0142 | 0.8010 ± 0.0077 | 0.6687 ± 0.0099 | 0.6571 ± 0.0118 | |
Levine32dim | Accense | 0.5514 ± 0.0794 | 0.6008 ± 0.0627 | 0.6876 ± 0.0389 | 0.5289 ± 0.0740 |
PhenoGraph | 0.6369 ± 0.0253 | 0.7062 ± 0.0213 | 0.7410 ± 0.0142 | 0.6437 ± 0.0240 | |
Xshift | 0.7543 ± 0.0605 | 0.7706 ± 0.0469 | 0.7690 ± 0.0323 | 0.7593 ± 0.0737 | |
kmeans | 0.5753 ± 0.0413 | 0.6748 ± 0.0231 | 0.7302 ± 0.0115 | 0.6405 ± 0.0638 | |
flowMeans | 0.9216 ± 0.0318 | 0.9279 ± 0.0337 | 0.9115 ± 0.0290 | 0.9397 ± 0.0342 | |
FlowSOM | 0.8787 ± 0.0975 | 0.8979 ± 0.0664 | 0.8840 ± 0.0600 | 0.8803 ± 0.1267 | |
DEPECHE | 0.8931 ± 0.0010 | 0.9231 ± 0.0009 | 0.8436 ± 0.0008 | 0.9297 ± 0.0009 | |
Muscle | Accense | 0.3687 ± 0.0663 | 0.4072 ± 0.0743 | 0.3953 ± 0.0391 | 0.2397 ± 0.0759 |
PhenoGraph | 0.3930 ± 0.0325 | 0.4336 ± 0.0249 | 0.3912 ± 0.0083 | 0.2694 ± 0.0261 | |
Xshift | 0.5119 ± 0.0591 | 0.5133 ± 0.0463 | 0.3882 ± 0.0190 | 0.3572 ± 0.0405 | |
kmeans | 0.6113 ± 0.0046 | 0.6207 ± 0.0045 | 0.4958 ± 0.0030 | 0.4243 ± 0.0055 | |
flowMeans | 0.7880 ± 0.0193 | 0.7928 ± 0.0089 | 0.5841 ± 0.0145 | 0.6364 ± 0.0347 | |
FlowSOM | 0.8210 ± 0.0068 | 0.8286 ± 0.0073 | 0.6470 ± 0.0072 | 0.6688 ± 0.0175 | |
DEPECHE | 0.8346 ± 0.0018 | 0.8850 ± 0.0019 | 0.5792 ± 0.0015 | 0.7074 ± 0.0035 | |
Samusik01 | Accense | 0.5868 ± 0.0502 | 0.6376 ± 0.0400 | 0.7165 ± 0.0237 | 0.5574 ± 0.0290 |
PhenoGraph | 0.9260 ± 0.0412 | 0.9249 ± 0.0344 | 0.8979 ± 0.0285 | 0.9250 ± 0.0526 | |
Xshift | 0.8909 ± 0.0485 | 0.9091 ± 0.0324 | 0.8742 ± 0.0196 | 0.8781 ± 0.0561 | |
kmeans | 0.4837 ± 0.0572 | 0.5535 ± 0.0401 | 0.6437 ± 0.0186 | 0.4655 ± 0.0482 | |
flowMeans | 0.9064 ± 0.0163 | 0.9099 ± 0.0163 | 0.8818 ± 0.0137 | 0.9206 ± 0.0045 | |
FlowSOM | 0.8386 ± 0.0693 | 0.8417 ± 0.0668 | 0.8185 ± 0.0639 | 0.8561 ± 0.0732 | |
DEPECHE | 0.8300 ± 0.0047 | 0.8677 ± 0.0047 | 0.7271 ± 0.0050 | 0.8298 ± 0.0068 | |