Table 2. Normalized average pairwise distances between cells with the same GO localization term in various feature spaces.

Feature Set	Normalized Average Pairwise Distance (Same Cell Lines)	Normalized Average Pairwise Distance (Different Cell Lines)	Difference
Classic	-0.3027	-0.1813	0.1214
Transfer Learning (VGG16)	-0.2525	-0.1515	0.1010
Autoencoder	-0.2486	-0.0965	0.1521
Paired Cell Inpainting (Conv3)	-0.4855	-0.3953	0.0902
Paired Cell Inpainting (Conv4)	-0.2656	-0.2271	0.0385

Normalized average pairwise distance scores between cells in image pairs with the same GO localization term, with the additional constraint of both images between from either the same cell line, or from different cell lines. We also report the difference between the two sets of scores; a smaller difference means that the model’s performance drops less when cell lines are different.