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Patch 1 #5

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fccebec
readme
IdoSpringer Jan 19, 2020
d47a54b
readme
IdoSpringer Jan 19, 2020
942f29b
updated figures
IdoSpringer Jun 19, 2020
3e05d09
updated README
IdoSpringer Jun 23, 2020
0c6a08b
README
IdoSpringer Jun 23, 2020
46bc47a
Update README.md
louzounlab Aug 25, 2020
43143ce
Update README.md
louzounlab Aug 25, 2020
0d27499
BUG FIX
IdoSpringer Aug 26, 2020
5c6fc37
Merge remote-tracking branch 'origin/master'
IdoSpringer Aug 26, 2020
6fdfcaf
Update lstm_utils.py
cirdeCyL Aug 18, 2022
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9 changes: 5 additions & 4 deletions ERGO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -358,8 +358,8 @@ def predict(args):
pep_atox = {amino: index for index, amino in enumerate(['PAD'] + amino_acids)}
tcr_atox = {amino: index for index, amino in enumerate(amino_acids + ['X'])}

if args.ae_file == 'auto':
args.ae_file = 'TCR_Autoencoder/tcr_ae_dim_30.pt'
# if args.ae_file == 'auto':
args.ae_file = 'TCR_Autoencoder/tcr_ae_dim_100.pt'
if args.model_file == 'auto':
dir = 'models'
p_key = 'protein' if args.protein else ''
Expand Down Expand Up @@ -387,13 +387,13 @@ def predict(args):
# Load model
device = args.device
if args.model_type == 'ae':
model = AutoencoderLSTMClassifier(10, device, 28, 21, 30, 50, args.ae_file, False)
model = AutoencoderLSTMClassifier(10, device, 28, 21, 100, 50, args.ae_file, False)
checkpoint = torch.load(args.model_file, map_location=device)
model.load_state_dict(checkpoint['model_state_dict'])
model.to(device)
model.eval()
if args.model_type == 'lstm':
model = DoubleLSTMClassifier(10, 30, 0.1, device)
model = DoubleLSTMClassifier(10, 500, 0.1, device)
checkpoint = torch.load(args.model_file, map_location=device)
model.load_state_dict(checkpoint['model_state_dict'])
model.to(device)
Expand Down Expand Up @@ -442,4 +442,5 @@ def predict(args):
elif args.function == 'predict':
predict(args)

# example
# python ERGO.py train lstm mcpas specific cuda:0 --model_file=model.pt --train_data_file=train_data --test_data_file=test_data
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