Table 4.

NMI scores based on SC3 clustering

Dataset	raw${}^{\ast }$	SIMLR	ZINB-WaVE	scImpute	DrImpute	SAVER	MAGIC	NE	scVI	DCA	scScope	SAUCIE
ILC	0.831	0.039	0.014	0.693	0.496	0.841	0.027	0.839	0.013	0.264	0.024	0.019
HCC	0.656	0.203	0.030	0.320	0.286	0.670	0.084	0.382	0.317	0.289	0.255	0.023
CRC	0.380	0.243	0.153	0.294	0.384	0.483	0.150	0.388	0.301	0.346	0.301	0.043
NSCLC	0.162	0.164	0.010	0.172	0.072	0.260	0.050	0.350	-	0.190	0.191	0.021
PBMC	0.821	0.814	0.760	0.780	0.802	0.830	0.703	0.831	0.853	0.833	0.891	0.211
BCC	0.603	0.475	0.460	–	–	0.503	0.113	0.525	0.556	0.546	0.398	0.090
ITC	0.599	0.554	0.585	0.433	0.545	0.556	0.172	0.493	0.466	0.408	0.228	0.087
DC.human	0.557	0.523	0.560	0.542	0.600	0.546	0.379	0.610	0.635	0.615	0.554	0.056
DC.mouse	0.685	0.471	0.698	0.509	0.690	0.690	0.328	0.600	0.666	0.618	0.437	0.171
Melanoma.1	0.557	0.498	0.564	0.466	0.625	0.616	0.208	0.507	0.488	0.536	0.544	0.064
Melanoma.2	0.526	0.422	–	–	0.516	0.412	0.342	0.440	0.517	-	0.054	0.101
BRCA	0.328	0.239	–	–	0.174	0.444	0.302	0.277	0.447	-	0.054	0.189
Sim1	0.780	0.988	0.543	0.982	1.000	0.902	0.594	0.973	0.147	0.925	0.918	0.324
Sim2	0.008	0.928	0.003	0.198	0.996	0.604	0.517	0.849	0.018	0.557	0.878	0.323
Sim3	0.004	0.422	0.002	0.074	0.920	0.010	0.353	0.591	0.032	0.214	0.872	0.166
Sim4	0.007	0.138	0.002	0.007	0.130	0.005	0.034	0.104	0.006	0.004	0.601	0.025

${}^{\ast }$ ’raw’ indicates data before imputation

${}^{\ast \ast }$ ’-’ means a method failed to finish imputation