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import pandas as pd |
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import pandas as pd |
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def train_DeepDRA(x_cell_train, x_cell_test, x_drug_train, x_drug_test, y_train, y_test, cell_sizes, drug_sizes): |
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def train_DeepDRA(x_cell_train, x_cell_test, x_drug_train, x_drug_test, y_train, y_test, cell_sizes, drug_sizes,device): |
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""" |
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""" |
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Train and evaluate the DeepDRA model. |
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Train and evaluate the DeepDRA model. |
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mlp_output_dim = 1 |
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mlp_output_dim = 1 |
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num_epochs = 25 |
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num_epochs = 25 |
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model = DeepDRA(cell_sizes, drug_sizes, ae_latent_dim, ae_latent_dim, mlp_input_dim, mlp_output_dim) |
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model = DeepDRA(cell_sizes, drug_sizes, ae_latent_dim, ae_latent_dim, mlp_input_dim, mlp_output_dim) |
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model.to(device) |
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# Step 3: Convert your training data to PyTorch tensors |
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# Step 3: Convert your training data to PyTorch tensors |
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x_cell_train_tensor = torch.Tensor(x_cell_train.values) |
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x_cell_train_tensor = torch.Tensor(x_cell_train.values) |
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x_drug_train_tensor = torch.Tensor(x_drug_train.values) |
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x_drug_train_tensor = torch.Tensor(x_drug_train.values) |
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y_train_tensor = torch.Tensor(y_train) |
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y_train_tensor = torch.Tensor(y_train) |
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y_train_tensor = y_train_tensor.unsqueeze(1) |
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y_train_tensor = y_train_tensor.unsqueeze(1) |
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x_cell_train_tensor.to(device) |
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x_drug_train_tensor.to(device) |
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y_train_tensor.to(device) |
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# Compute class weights |
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# Compute class weights |
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classes = [0, 1] # Assuming binary classification |
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classes = [0, 1] # Assuming binary classification |
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class_weights = torch.tensor(compute_class_weight(class_weight='balanced', classes=classes, y=y_train), |
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class_weights = torch.tensor(compute_class_weight(class_weight='balanced', classes=classes, y=y_train), |
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train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=True) |
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train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=True) |
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val_loader = DataLoader(val_dataset, batch_size=batch_size, shuffle=True) |
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val_loader = DataLoader(val_dataset, batch_size=batch_size, shuffle=True) |
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# Step 6: Train the model |
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# Step 6: Train the model |
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train(model, train_loader, val_loader, num_epochs,class_weights) |
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train(model, train_loader, val_loader, num_epochs,class_weights) |
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Returns: |
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Returns: |
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- history (dict): Dictionary containing evaluation metrics for each run. |
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- history (dict): Dictionary containing evaluation metrics for each run. |
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""" |
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""" |
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device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu") |
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print(torch.cuda.is_available()) |
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torch.zeros(1).cuda() |
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# Step 1: Initialize a dictionary to store evaluation metrics |
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# Step 1: Initialize a dictionary to store evaluation metrics |
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history = {'AUC': [], 'AUPRC': [], "Accuracy": [], "Precision": [], "Recall": [], "F1 score": []} |
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history = {'AUC': [], 'AUPRC': [], "Accuracy": [], "Precision": [], "Recall": [], "F1 score": []} |
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# Step 7: Train and evaluate the DeepDRA model on test data |
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# Step 7: Train and evaluate the DeepDRA model on test data |
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results = train_DeepDRA(X_cell_train, X_cell_test, X_drug_train, X_drug_test, y_train, y_test, cell_sizes, |
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results = train_DeepDRA(X_cell_train, X_cell_test, X_drug_train, X_drug_test, y_train, y_test, cell_sizes, |
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drug_sizes) |
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drug_sizes, device) |
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else: |
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else: |
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# Step 8: Split the data into training and validation sets |
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# Step 8: Split the data into training and validation sets |
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X_cell_train, X_cell_test, X_drug_train, X_drug_test, y_train, y_test = train_test_split(X_cell_train, |
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X_cell_train, X_cell_test, X_drug_train, X_drug_test, y_train, y_test = train_test_split(X_cell_train, |
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shuffle=True) |
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shuffle=True) |
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# Step 9: Train and evaluate the DeepDRA model on the split data |
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# Step 9: Train and evaluate the DeepDRA model on the split data |
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results = train_DeepDRA(X_cell_train, X_cell_test, X_drug_train, X_drug_test, y_train, y_test, cell_sizes, |
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results = train_DeepDRA(X_cell_train, X_cell_test, X_drug_train, X_drug_test, y_train, y_test, cell_sizes, |
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drug_sizes) |
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drug_sizes, device) |
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# Step 10: Add results to the history dictionary |
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# Step 10: Add results to the history dictionary |
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Evaluation.add_results(history, results) |
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Evaluation.add_results(history, results) |