Two-dimensional UMAP plots of contextualized protein representations generated by PINNACLE from six different cell type contexts: bronchial vessel endothelial cell. Each dot is a protein representation. Colored dots indicate cell type context regions, and gray dots represent proteins from other cell types. Each protein embedding region is expected to be enriched neighborhoods that are spatially localized according to cell type context. To quantify this, we compute spatial enrichment of each protein embedding region using SAFE 31 and provide the mean and max neighborhood enrichment scores (NES) and the number of enriched neighborhoods output by the tool (Metrics and statistical analyses section in Methods and Extended Data Figs. 3 and 4 ).
