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add GAT to CLI #147

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add GAT to CLI #147

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10 changes: 5 additions & 5 deletions flexynesis/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ def print_full_help():
"usage: flexynesis [-h] --data_path DATA_PATH --model_class "
"{DirectPred,supervised_vae,MultiTripletNetwork,CrossModalPred,GNN,"
"RandomForest,SVM,XGBoost,RandomSurvivalForest} "
"[--gnn_conv_type {GC,GCN,SAGE}] [--target_variables TARGET_VARIABLES] "
"[--gnn_conv_type {GC,GCN,SAGE,GAT}] [--target_variables TARGET_VARIABLES] "
"[--covariates COVARIATES] [--surv_event_var SURV_EVENT_VAR] "
"[--surv_time_var SURV_TIME_VAR] [--config_path CONFIG_PATH] "
"[--fusion_type {early,intermediate}] [--hpo_iter HPO_ITER] "
Expand Down Expand Up @@ -130,7 +130,7 @@ def print_full_help():
"CrossModalPred,GNN,RandomForest,SVM,XGBoost,RandomSurvivalForest}"
)
print(" (Required) The kind of model class to instantiate")
print(" --gnn_conv_type {GC,GCN,SAGE}")
print(" --gnn_conv_type {GC,GCN,SAGE,GAT}")
print(
" If model_class is set to GNN, choose which graph "
"convolution type to use"
Expand Down Expand Up @@ -337,7 +337,7 @@ def main():
**Required** for training.

--gnn_conv_type (str):
If `--model_class=GNN`, choose graph convolution: ["GC", "GCN", "SAGE"].
If `--model_class=GNN`, choose graph convolution: ["GC", "GCN", "SAGE", "GAT"].

--target_variables (str):
Comma-separated target variables from `clin.csv`. Optional if survival
Expand Down Expand Up @@ -534,7 +534,7 @@ def main():
parser.add_argument(
"--gnn_conv_type",
type=str,
choices=["GC", "GCN", "SAGE"],
choices=["GC", "GCN", "SAGE", "GAT"],
help="If model_class is set to GNN, choose which graph convolution type to use",
)
parser.add_argument(
Expand Down Expand Up @@ -1047,7 +1047,7 @@ def main():
if args.model_class == "GNN":
if not args.gnn_conv_type:
warnings.warn(
"\n\n!!! When running GNN, set --gnn_conv_type (GC/GCN/SAGE). "
"\n\n!!! When running GNN, set --gnn_conv_type (GC/GCN/SAGE/GAT). "
"Falling back to GC !!!\n"
)
time.sleep(3)
Expand Down
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