Table 1 .

MMDs of the CyTOF data before and after being calibrated by individual methods

	Raw	ComBat	Ratio_G	fSVA	ResNet	NormAE	Ours	In Batch 1	In Batch 2
Patient 1	0.243 ± 0.010	0.167 ± 0.006	0.243 ± 0.010	–	0.116 ± 0.008	0.113 ± 0.005	0.067 ± 0.005	0.053 ± 0.005	0.057 ± 0.005
Patient 2	0.230 ± 0.010	0.139 ± 0.005	0.230 ± 0.010	0.158 ± 0.007	0.120 ± 0.009	0.131 ± 0.007	0.092 ± 0.005	0.065 ± 0.006	0.064 ± 0.005

“Raw” represents the MMD value of the source and target batches before calibration. “—” means that the fSVA method has collapsed due to numerical singularity in our computation. “In Batch 1 (or 2)” represents the intrinsic MMD without being corrupted by batch effect inside each batch