Table 1.

Comparison of mean and standard deviation of running time (seconds) between models

Modela	Simulationb	GTEx Z score	Perturb-seq
SuSiE PCA	3.14(0.49)	1.20	68.11
Sparse PCA	51.96(33.50)	41.22	1213.21
EBMF	39.83(5.80)	498.60	243.03

^aAll run time data in the table are based on the analyses performed on the same CPU for consistency. The CPU we used is the Apple M2 chip with 16 GB memory.

^bRun time for simulation is recorded based on simulation setting in Figure 1, i.e., $N=1000,P=6000,K=4,L=40$; the average run time and corresponding standard deviation are computed for 100 simulations. We presented a more detailed run time comparison in simulation in Figure S4.