ctheodoris

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Geneformer

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Thanks for your question! The "cls_and_gene" mode is for determining the impact of gene deletion on the cell embedding as a whole (cls) as well as the other genes in the cell (gene). If you are trying to perform perturbations comparing the impact of a gene on other genes, you do not need to provide cell_states_to_model and state_embs_dict, as this is not relevant to the gene to gene interaction. I would suggest trying without that if you are interested in quantifying gene shifts.