Gap between embedding similarities using PINNACLEs protein representations (a) and a noncontextualized model’s protein representations (b) on n = 394,760 samples (that is, cell type-specific protein representations). Similarities are calculated between pairs of proteins in the same cell type (dark shade of color) or different cell types (light shade of color), and stratified by the compartment from which the cell types are derived. We use the two-sided two-sample Kolmogorov–Smirnov test for goodness of fit. Annotations indicate median values. The noncontextualized model is an ablated version of PINNACLE without any notion of tissue or cell type organization (that is, remove cell type and tissue network and all cell type- and tissue-related components of PINNACLEs architecture and objective function). The bounds of the box show the quartiles of the data, the center indicates the median value of the data and the whiskers represent the farthest data point within 1.5 x interquartile range.
