ctheodoris

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Geneformer

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Hello,

I've had success outputting cosine shifts in cell embeddings when running emb_mode="cell" with the parameters listed below; however, when changing emb_mode="cell_and_gene" and keeping all other parameters unchanged, I get the exact same output (cosine shifts in cell embeddings only).

My goal is to observe how all other gene embeddings are affected after a single gene perturbation, to identify important proteins in a network (similar to Fig5a/b in the paper). I'm currently using a small subset from the Genecorpus-30M dataset as my input data.

How should I change my parameters to get gene embedding outputs?

Thank you!

# Set perturbation parameters
isp = InSilicoPerturber(perturb_type="delete",
                        perturb_rank_shift=None,
                        genes_to_perturb=["ENSG00000196262"],
                        combos=0,
                        anchor_gene=None,
                        model_type="Pretrained",
                        num_classes=0,
                        emb_mode="cell",
                        cell_emb_style="mean_pool",
                        filter_data=None,
                        cell_states_to_model=None,
                        max_ncells=None,
                        cell_inds_to_perturb={"start":0, "end":50},
                        emb_layer=-1,
                        forward_batch_size=50,
                        nproc=16,
                        token_dictionary_file = "/home/ubuntu/Geneformer/geneformer/token_dictionary.pkl")

# Perturb data
isp.perturb_data("/home/ubuntu/Geneformer/",
                 "/data/genecorpus_filtered_nonhep/",
                 "/data/genecorpus_filtered_nonhep/delete_cell/",
                 "cell_and_gene_test_PPIA")

# Set perturbation stats
ispstats = InSilicoPerturberStats(mode="aggregate_data",
                                  genes_perturbed=["ENSG00000196262"],
                                  combos=0,
                                  anchor_gene=None,
                                  cell_states_to_model=None,
                                  token_dictionary_file = "/home/ubuntu/Geneformer/geneformer/token_dictionary.pkl")

# Get perturbation stats
ispstats.get_stats("/data/genecorpus_filtered_nonhep/delete_cell/",
                   None,
                   "/data/genecorpus_filtered_nonhep/delete_cell/",
                   "delete_cell_and_gene_test_PPIA")