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Table 4 Average retrieval performance across the different cell type

From: Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data

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