ctheodoris/Geneformer · In silico perturbation error with combos

Apr 8

Hello,

In silico perturbation using a fine-tuned model with combos=0 successfully worked.
However, when I set combos=1 in the same setting, isp.perturb_data() had an error maybe due to dimension mismatch.
Could you teach me what was happened?
I updated geneformer on Feb 8, 2024.

isp = InSilicoPerturber(perturb_type="overexpress",
                        perturb_rank_shift=None,
                        genes_to_perturb="all",
                        combos=1,
                        anchor_gene=None,
                        model_type="CellClassifier",
                        num_classes=5,
                        emb_mode="cell",
                        cell_emb_style="mean_pool",
                        filter_data=None,
                        cell_states_to_model={
                            "state_key": "label",
                            "start_state": 0,
                            "goal_state": goal_state,
                            "alt_states": []},
                        max_ncells=None,
                        emb_layer=0,
                        cell_inds_to_perturb="all",
                        forward_batch_size=40,
                        nproc=8)

num = 0 # No. of splitted datasets

isp.perturb_data("Norman/finetune/231214_geneformer_CellClassifier_K562_L2048_B12_LR0.0006454238554420985_LSlinear_WU126.5101151044998_E10_Oadamw_F0",
                 "Norman/data_split_for_perturb_selected_combo/select_{}_to_{}.dataset/".format(num, num+400),
                 "Norman/perturb_select_results_freeze-4/overexpress_{}/".format(gene),
                 "perturbed_{}_to_{}".format(num, num+400))

Outputs:

davidjwen

Jun 7

Thanks for raising this issue! We don't currently support the combinations of combos=1 and anchor_gene=None, given the computational complexity of perturbing all pairs of genes. If you are still interested in perturbing combinations, please specify the anchor_gene. Hope that helps!

tasahi-1 changed discussion status to closed Jun 8