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missing modality #7

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14 changes: 10 additions & 4 deletions utils/core_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -495,7 +495,7 @@ def _calculate_metrics(loader, dataset_factory, survival_train, all_risk_scores,
return c_index, c_index_ipcw, BS, IBS, iauc


def _summary(dataset_factory, model, omics_format, loader, loss_fn, survival_train=None):
def _summary(args,dataset_factory, model, omics_format, loader, loss_fn, survival_train=None):
r"""
Run a validation loop on the trained model

Expand Down Expand Up @@ -538,6 +538,12 @@ def _summary(dataset_factory, model, omics_format, loader, loss_fn, survival_tra

data_WSI, mask, y_disc, event_time, censor, data_omics, clinical_data_list, mask = _unpack_data(omics_format, device, data)

if args.modality == "G":
data_WSI = torch.zeros_like(data_WSI)
elif args.modality == "P":
data_omics = torch.zeros_like(data_omics)
elif args.modality == "Both":
pass
input_args = {"x_wsi": data_WSI.to(device)}
input_args["return_attn"] = False
input_args["y"] = None
Expand Down Expand Up @@ -639,7 +645,7 @@ def _step(cur, args, loss_fn, model, optimizer, train_loader, val_loader, log_fi

for epoch in range(args.max_epochs):
_train_loop_survival(args, epoch, model, args.omics_format, train_loader, optimizer, loss_fn, log_file)
results_dict, val_cindex, val_cindex_ipcw, val_BS, val_IBS, val_iauc, total_loss = _summary(args.dataset_factory,
results_dict, val_cindex, val_cindex_ipcw, val_BS, val_IBS, val_iauc, total_loss = _summary(args,args.dataset_factory,
model, args.omics_format, val_loader, loss_fn, all_survival)
print(
'Epoch:{} Val c-index: {:.4f} | Final Val c-index2: {:.4f} | Final Val IBS: {:.4f} | Final Val iauc: {:.4f}'.format(
Expand Down Expand Up @@ -667,7 +673,7 @@ def _step(cur, args, loss_fn, model, optimizer, train_loader, val_loader, log_fi
# save the trained model
torch.save(model.state_dict(), os.path.join(args.results_dir, "s_{}_checkpoint.pth".format(cur)))

results_dict, val_cindex, val_cindex_ipcw, val_BS, val_IBS, val_iauc, total_loss = _summary(args.dataset_factory, model, args.omics_format, val_loader, loss_fn, all_survival)
results_dict, val_cindex, val_cindex_ipcw, val_BS, val_IBS, val_iauc, total_loss = _summary(args,args.dataset_factory, model, args.omics_format, val_loader, loss_fn, all_survival)

print('Final Val c-index: {:.4f} | Final Val c-index2: {:.4f} | Final Val IBS: {:.4f} | Final Val iauc: {:.4f}'.format(
val_cindex,
Expand All @@ -684,7 +690,7 @@ def _step(cur, args, loss_fn, model, optimizer, train_loader, val_loader, log_fi

best_model = torch.load(os.path.join(args.results_dir, "model_best_s{}.pth".format(cur)))
model.load_state_dict(best_model)
_, val_cindex, val_cindex_ipcw, val_BS, val_IBS, val_iauc, total_loss = _summary(args.dataset_factory, model, args.omics_format, val_loader, loss_fn, all_survival)
_, val_cindex, val_cindex_ipcw, val_BS, val_IBS, val_iauc, total_loss = _summary(args,args.dataset_factory, model, args.omics_format, val_loader, loss_fn, all_survival)
print('Best Val c-index: {:.4f} | Best Val c-index2: {:.4f} | Best Val IBS: {:.4f} | Best Val iauc: {:.4f}'.format(
val_cindex,
val_cindex_ipcw,
Expand Down
1 change: 1 addition & 0 deletions utils/process_args.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,7 @@ def _process_args():

#---> model related
parser.add_argument('--method', type=str, default="PIBD", help='methd type')
parser.add_argument('--modality', type=str, choices=["Both", "G", "P"],default="Both", help='existing modality, designed for missing modality')
parser.add_argument('--encoding_dim', type=int, default=768, help='WSI encoding dim (1024 for resnet50, 768 for swin)')
parser.add_argument('--wsi_projection_dim', type=int, default=256, help="projection dim of features")
parser.add_argument('--omics_format', type=str, default="pathways", choices=["gene","groups","pathways"], help='format of omics data')
Expand Down