Table 3.

Unknown cell-type clustering performance of the different models analyzed for the LPGO experiments (P = 4). Although our pathway-based models are nearly ten times smaller (sparse), the performance is very close to the PPI-based NN. The mean of 20 splits was reported

Architecture	Number of nodes (2nd hidden layer)	Homogeneity	Completeness	V-measure	ARI	AMI	Fowlkes-Mallows	Average
Dense	–	0.801	0.799	0.798	0.725	0.786	0.814	0.787
Dense with pathways	–	0.804	0.797	0.798	0.718	0.786	0.811	0.786
Dense with PPI	–	0.811	0.804	0.805	0.728	0.794	0.817	0.793
Dense with PPI and GRN	–	0.820	0.808	0.812	0.746	0.802	0.827	0.802
Signaling pathways	–	0.797	0.788	0.790	0.716	0.778	0.809	0.780
Signaling pathways	100	0.775	0.803	0.786	0.729	0.774	0.820	0.781