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Table 1.

Empirical run time of label-free marker gene selection methods on omics data sets

	DLPFC	CBMC	scFFPE BC	Mouse brain
geneCover	22.1 sec	18.3 sec	35.4 sec	134.7 sec
geneBasis	515.4 sec	2193.2 sec	17.5 h	93.8 h
SCMER	241.6 sec	1961.4 sec	2.4 h	18.2 h
PERSIST	3.8 h	7.5 h	5.5 h	N/A

[i] The time is measured in either seconds (sec) or hours (h). For each method, we obtained 100 markers for the DLPFC and CBMC data sets, 300 markers for the scFFPE breast cancer data set ( ${k_{t}}_{1 : T} = {100, 100, 100}$ , $m = 3$ for geneCover), and 200 markers for the mouse brain Visium HD data set ( ${k_{t}}_{1 : T} = {80, 60, 60}$ , $m = 3$ for geneCover). geneCover and geneBasis were run using the Intel Core i9 13900K CPU, whereas SCMER and PERSIST were run on the NVIDIA GeForce RTX 4090 GPU. (N/A) memory overflow.