import os
[docs]
def get_mousebrain_h3k27ac_base_config(run_name="mousebrain_H3K27ac_run4"):
output_dir = f"/data/xiongsc/projects/SMODER/outputs/{run_name}"
model_save_dir = os.path.join(output_dir, "trained_models")
base_config = {
"sc_rna_path": "/data/xiongsc/data/SMODER/mousebrain_H3K27ac/sc_mousebrain_processed.h5ad",
"st_rna_path": "/data/xiongsc/data/SMODER/mousebrain_H3K27ac/RNA.h5ad",
"st_adt_path": "/data/xiongsc/data/SMODER/mousebrain_H3K27ac/peak.h5ad",
"output_dir": output_dir,
"model_save_dir": model_save_dir,
}
os.makedirs(base_config["output_dir"], exist_ok=True)
os.makedirs(base_config["model_save_dir"], exist_ok=True)
return base_config
[docs]
def get_mousebrain_h3k27ac_params():
params = {
"ref_celltype_col": "annotation_1",
"sample_id_col": "sample",
"log_FC": 1.25,
"do_select_info_genes": True,
"ct_select": None,
"modal2_type": "peak",
"K_spatial": 8,
"K_feature": 8,
"pca_n_components_rna": 256,
"modal2_target_dim": 256,
"obsm_name_rna": "X_feat_rna",
"obsm_name_modal2": "X_feat_modal2",
"method": 2,
"embd_dim": 50,
"epochs": 10000,
"learning_rate": 2e-3,
"hidden_dim": 512,
"weight_loss": [1, 0.001],
"weight_consistency": 1,
"weight_spatial": 1e-5,
"seed": 1,
"model_save": True,
"device": "cuda:0",
}
return params