The NicheFormer paper introduced a task of predicting neighboring cells' gene-expression states from a cell's gene-expression state.

“Whereas if you ask a bit or if you wanna predict a cell type or something like that, you know, for that mostly logistic regression is fine. But if you wanna predict something a bit more difficult, for example, in our NicheFormer paper, which is a foundation model for spatial omics, we showed we had a new task which we introduced where you say you have a, you have the gene expression, you have sort of this state, a latent space of a single cell.”

“Can you predict the gene expression state of its neighboring cells? Because you know, they're always in communication or maybe the other way around. So like they're always in communication. So because, you know, they talk to each other, you sort of see a remnant of that sort of cell state in this one.”