Table 4.

Average retrieval performance across the different cell type

Architecture	Number of nodes (2nd layer)	HSC	4cell	ICM	Spleen	8cell	Neuron	Zygote	2cell	ESC	Mean
PCA 100 (with full gene space)	–	0.181	0.669	0.026	0.975	0.176	0.627	0.462	0.675	0.106	0.433
PCA 100 (with signaling gene space)	–	0.179	0.561	0.128	0.989	0.191	0.624	0.455	0.676	0.205	0.445
Dense	–	0.243	0.643	0.000	0.734	0.147	0.404	0.569	0.514	0.148	0.378
Dense with signaling pathways	–	0.259	0.648	0.000	0.849	0.236	0.486	0.509	0.656	0.130	0.419
Dense with PPI	–	0.196	0.638	0.041	0.927	0.212	0.550	0.575	0.686	0.179	0.445
Dense with PPI/GRN	–	0.194	0.645	0.007	0.930	0.294	0.542	0.600	0.711	0.190	0.457
Dense with PPI/GRN	100	0.068	0.771	0.182	0.956	0.849	0.561	0.415	0.553	0.710	0.563
Signaling pathways (+)	–	0.163	0.438	0.011	0.619	0.179	0.475	0.344	0.465	0.128	0.314
Signaling pathways (+)	100	0.149	0.307	0.050	0.402	0.198	0.352	0.592	0.368	0.137	0.284
Signaling pathways (parameter tuning) (+)	–	0.107	0.768	0.049	0.960	0.625	0.549	0.471	0.627	0.110	0.474
Signaling pathways (parameter tuning) (+)	Size*	0.155	0.803	0.117	0.955	0.568	0.550	0.497	0.623	0.150	0.491
scvis	–	0.203	0.522	0.000	0.813	0.077	0.733	0.424	0.683	0.512	0.441

*The size of second layer (size) is defined after tuning in hyperparameter tuning networks