graphdrp_params.txt

[Global_Params]
model_name = "GraphDRP"

[Preprocess]
train_split_file = "GDSCv1_split_0_train.txt"
val_split_file = "GDSCv1_split_0_val.txt"
test_split_file = "GDSCv1_split_0_test.txt"
ml_data_outdir = "./ml_data/GDSCv1-GDSCv1/split_0"
data_format = ".pt"
y_data_files = [["response.tsv"]]
x_data_canc_files = [["cancer_gene_expression.tsv", ["Gene_Symbol"]]]
x_data_drug_files = [["drug_SMILES.tsv"]]
use_lincs = True
scaling = "std"

[Train]
train_ml_data_dir = "./ml_data/GDSCv1-GDSCv1/split_0"
val_ml_data_dir = "./ml_data/GDSCv1-GDSCv1/split_0"
model_outdir = "./out_models/GDSCv1/split_0"
model_file_name = "model"
model_file_format = ".pt"
epochs = 150
batch_size = 256
val_batch = 256
loss = "mse"
early_stop_metric = "mse"
patience = 20
ckpt_save_interval = 5
model_arch = "GINConvNet"
log_interval = 20
cuda_name = "cuda:7"

[Infer]
test_ml_data_dir = "./ml_data/GDSCv1-GDSCv1/split_0"
model_dir = "./out_models/GDSCv1/split_0"
infer_outdir = "./out_infer/GDSCv1-GDSCv1/split_0"
test_batch = 256
cuda_name = "cuda:7"