feat: add main files

DeepDRA.py

@@ -88,7 +88,7 @@ class DeepDRA(nn.Module):
         return torch.square(w).sum()
 
 
-def train(model, train_loader, num_epochs):
+def train(model, train_loader, val_loader,  num_epochs,class_weights):
     """
     Trains the DeepDRA (Deep Drug Response Anticipation) model.
 
@@ -97,23 +97,44 @@ def train(model, train_loader, num_epochs):
     - train_loader (DataLoader): DataLoader for the training dataset.
     - num_epochs (int): Number of training epochs.
     """
+
+
     autoencoder_loss_fn = nn.MSELoss()
     mlp_loss_fn = nn.BCELoss()
 
-    mlp_optimizer = optim.Adam(model.parameters(), lr=0.0005)
+    train_accuracies = []
+    val_accuracies = []
+
+    train_loss = []
+    val_loss = []
+
+    mlp_optimizer = optim.Adam(model.parameters(), lr=0.0005,)
     scheduler = lr_scheduler.ReduceLROnPlateau(mlp_optimizer, mode='min', factor=0.8, patience=5, verbose=True)
 
+    # Define weight parameters for each loss term
+    cell_ae_weight = 1.0
+    drug_ae_weight = 1.0
+    mlp_weight = 1.0
+
     for epoch in range(num_epochs):
+        model.train()
+        total_train_loss = 0.0
+        train_correct = 0
+        train_total_samples = 0
         for batch_idx, (cell_data, drug_data, target) in enumerate(train_loader):
             mlp_optimizer.zero_grad()
 
             # Forward pass
             cell_decoded_output, drug_decoded_output, mlp_output = model(cell_data, drug_data)
 
+            # Compute class weights for the current batch
+            # batch_class_weights = class_weights[target.long()]
+            # mlp_loss_fn = nn.BCEWithLogitsLoss(weight=batch_class_weights)
+
             # Compute losses
-            cell_ae_loss = autoencoder_loss_fn(cell_decoded_output, cell_data)
-            drug_ae_loss = autoencoder_loss_fn(drug_decoded_output, drug_data)
-            mlp_loss = mlp_loss_fn(mlp_output, target)
+            cell_ae_loss = cell_ae_weight * autoencoder_loss_fn(cell_decoded_output, cell_data)
+            drug_ae_loss = drug_ae_weight * autoencoder_loss_fn(drug_decoded_output, drug_data)
+            mlp_loss = mlp_weight * mlp_loss_fn(mlp_output, target)
 
             # Total loss is the sum of autoencoder losses and MLP loss
             total_loss = drug_ae_loss + cell_ae_loss + mlp_loss
@@ -121,14 +142,56 @@ def train(model, train_loader, num_epochs):
             # Backward pass and optimization
             total_loss.backward()
             mlp_optimizer.step()
+            total_train_loss += total_loss.item()
+
+            # Calculate accuracy
+            train_predictions = torch.round(mlp_output)
+            train_correct += (train_predictions == target).sum().item()
+            train_total_samples += target.size(0)
+
+        avg_train_loss = total_train_loss / len(train_loader)
+        train_loss.append(avg_train_loss)
+
+        # Validation
+        model.eval()
+        total_val_loss = 0.0
+        correct = 0
+        total_samples = 0
+        with torch.no_grad():
+            for val_batch_idx, (cell_data_val, drug_data_val, val_target) in enumerate(val_loader):
+                cell_decoded_output_val, drug_decoded_output_val, mlp_output_val = model(cell_data_val, drug_data_val)
+                # batch_class_weights = class_weights[val_target.long()]
+                # mlp_loss_fn = nn.BCEWithLogitsLoss(weight=batch_class_weights)
+
+                # Compute losses
+                cell_ae_loss_val = cell_ae_weight * autoencoder_loss_fn(cell_decoded_output_val, cell_data_val)
+                drug_ae_loss_val = drug_ae_weight * autoencoder_loss_fn(drug_decoded_output_val, drug_data_val)
+                mlp_loss_val = mlp_weight * mlp_loss_fn(mlp_output_val, val_target)
+
+                # Total loss is the sum of autoencoder losses and MLP loss
+                total_val_loss = drug_ae_loss_val + cell_ae_loss_val + mlp_loss_val
+
+                # Calculate accuracy
+                val_predictions = torch.round(mlp_output_val)
+                correct += (val_predictions == val_target).sum().item()
+                total_samples += val_target.size(0)
+
+            avg_val_loss = total_val_loss / len(val_loader)
+            val_loss.append(avg_val_loss)
+
+
+        train_accuracy = train_correct / train_total_samples
+        train_accuracies.append(train_accuracy)
+        val_accuracy = correct / total_samples
+        val_accuracies.append(val_accuracy)
 
-            # Print progress
-            if batch_idx % 200 == 0:
-                print('Epoch [{}/{}], Total Loss: {:.4f}'.format(
-                    epoch + 1, num_epochs, total_loss.item()))
+        print(
+            'Epoch [{}/{}], Train Loss: {:.4f}, Val Loss: {:.4f}, Train Accuracy: {:.4f}, Val Accuracy: {:.4f}'.format(
+                epoch + 1, num_epochs, avg_train_loss, avg_val_loss, train_accuracy,
+                val_accuracy))
 
         # Learning rate scheduler step
-        scheduler.step(total_loss)
+        scheduler.step(total_train_loss)
 
     # Save the trained model
     torch.save(model.state_dict(), MODEL_FOLDER + 'DeepDRA.pth')

README.md

@@ -1 +1,8 @@
 # DeepDRA
+Data
+
+Download data from this link: https://drive.google.com/drive/folders/1-PgwD7KN9ZxCYBhyGAs3ihlbKK7s9jiO?usp=sharing
+
+Run
+
+You can run the main code with different data sets

evaluation.py

@@ -72,11 +72,11 @@ class Evaluation:
 
         # Step 2: Calculate and print AUC
         fpr, tpr, thresholds = metrics.roc_curve(all_targets, mlp_output)
-        auc = np.round(metrics.auc(fpr, tpr), 2)
+        auc = np.round(metrics.auc(fpr, tpr), 3)
 
         # Step 3: Calculate and print AUPRC
         precision, recall, thresholds = metrics.precision_recall_curve(all_targets, mlp_output)
-        auprc = np.round(metrics.auc(recall, precision), 2)
+        auprc = np.round(metrics.auc(recall, precision), 3)
 
         # Step 4: Print accuracy, AUC, AUPRC, and confusion matrix
         accuracy = accuracy_score(all_targets, all_predictions)
@@ -162,4 +162,11 @@ class Evaluation:
         avg_auc = np.mean(result_list['AUC'])
         avg_auprc = np.mean(result_list['AUPRC'])
         std_auprc = np.std(result_list['AUPRC'])
+        avg_accuracy = np.mean(result_list['Accuracy'])
+        avg_precision = np.mean(result_list['Precision'])
+        avg_recal = np.mean(result_list['Recall'])
+        avg_f1score = np.mean(result_list['F1 score'])
+        print(
+            f'AVG: Accuracy: {avg_accuracy:.3f}, Precision: {avg_precision:.3f}, Recall: {avg_recal:.3f}, F1 score: {avg_f1score:.3f}, AUC: {avg_auc:.3f}, ,AUPRC: {avg_auprc:.3f}')
+
         print(" Average AUC: {:.3f} \t Average AUPRC: {:.3f} \t Std AUPRC: {:.3f}".format(avg_auc, avg_auprc, std_auprc))

main.py

@@ -1,5 +1,6 @@
 from imblearn.under_sampling import RandomUnderSampler
 from sklearn.model_selection import train_test_split
+from sklearn.utils.class_weight import compute_class_weight
 
 from torch.utils.data import TensorDataset, DataLoader, SubsetRandomSampler
 
@@ -39,7 +40,7 @@ def train_DeepDRA(x_cell_train, x_cell_test, x_drug_train, x_drug_test, y_train,
     ae_latent_dim = 50
     mlp_input_dim = 2 * ae_latent_dim
     mlp_output_dim = 1
-    num_epochs = 20
+    num_epochs = 25
     model = DeepDRA(cell_sizes, drug_sizes, ae_latent_dim, ae_latent_dim, mlp_input_dim, mlp_output_dim)
 
     # Step 3: Convert your training data to PyTorch tensors
@@ -50,20 +51,34 @@ def train_DeepDRA(x_cell_train, x_cell_test, x_drug_train, x_drug_test, y_train,
     y_train_tensor = torch.Tensor(y_train)
     y_train_tensor = y_train_tensor.unsqueeze(1)
 
+    # Compute class weights
+    classes = [0, 1]  # Assuming binary classification
+    class_weights = torch.tensor(compute_class_weight(class_weight='balanced', classes=classes, y=y_train),
+                                 dtype=torch.float32)
+
+
+    x_cell_train_tensor, x_cell_val_tensor, x_drug_train_tensor, x_drug_val_tensor, y_train_tensor, y_val_tensor = train_test_split(
+        x_cell_train_tensor, x_drug_train_tensor, y_train_tensor, test_size=0.1,
+        random_state=RANDOM_SEED,
+        shuffle=True)
+
     # Step 4: Create a TensorDataset with the input features and target labels
     train_dataset = TensorDataset(x_cell_train_tensor, x_drug_train_tensor, y_train_tensor)
+    val_dataset = TensorDataset(x_cell_val_tensor, x_drug_val_tensor, y_val_tensor)
 
     # Step 5: Create the train_loader
     train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=True)
+    val_loader = DataLoader(val_dataset, batch_size=batch_size, shuffle=True)
+
 
     # Step 6: Train the model
-    train(model, train_loader, num_epochs=num_epochs)
+    train(model, train_loader, val_loader, num_epochs,class_weights)
 
     # Step 7: Save the trained model
-    torch.save(model,  MODEL_FOLDER + 'DeepDRA.pth')
+    torch.save(model, 'DeepDRA.pth')
 
     # Step 8: Load the saved model
-    model = torch.load( MODEL_FOLDER + 'DeepDRA.pth')
+    model = torch.load('DeepDRA.pth')
 
     # Step 9: Convert your test data to PyTorch tensors
     x_cell_test_tensor = torch.Tensor(x_cell_test.values)
@@ -99,8 +114,8 @@ def run(k, is_test=False):
 
     # Step 2: Load training data
     train_data, train_drug_screen = RawDataLoader.load_data(data_modalities=DATA_MODALITIES,
-                                                            raw_file_directory=GDSC_RAW_DATA_FOLDER,
-                                                            screen_file_directory=GDSC_SCREENING_DATA_FOLDER,
+                                                            raw_file_directory=RAW_BOTH_DATA_FOLDER,
+                                                            screen_file_directory=BOTH_SCREENING_DATA_FOLDER,
                                                             sep="\t")
 
     # Step 3: Load test data if applicable
@@ -117,18 +132,19 @@ def run(k, is_test=False):
     X_cell_train, X_drug_train, y_train, cell_sizes, drug_sizes = RawDataLoader.prepare_input_data(train_data,
                                                                                                    train_drug_screen)
 
+    rus = RandomUnderSampler(sampling_strategy="majority", random_state=RANDOM_SEED)
+    dataset = pd.concat([X_cell_train, X_drug_train], axis=1)
+    dataset.index = X_cell_train.index
+    dataset, y_train = rus.fit_resample(dataset, y_train)
+    X_cell_train = dataset.iloc[:, :sum(cell_sizes)]
+    X_drug_train = dataset.iloc[:, sum(cell_sizes):]
+
     # Step 5: Loop over k runs
     for i in range(k):
         print('Run {}'.format(i))
 
         # Step 6: If is_test is True, perform random under-sampling on the training data
         if is_test:
-            rus = RandomUnderSampler(sampling_strategy="majority", random_state=RANDOM_SEED)
-            dataset = pd.concat([X_cell_train, X_drug_train], axis=1)
-            dataset.index = X_cell_train.index
-            dataset, y_train = rus.fit_resample(dataset, y_train)
-            X_cell_train = dataset.iloc[:, :sum(cell_sizes)]
-            X_drug_train = dataset.iloc[:, sum(cell_sizes):]
 
             # Step 7: Train and evaluate the DeepDRA model on test data
             results = train_DeepDRA(X_cell_train, X_cell_test, X_drug_train, X_drug_test, y_train, y_test, cell_sizes,
@@ -138,7 +154,7 @@ def run(k, is_test=False):
             X_cell_train, X_cell_test, X_drug_train, X_drug_test, y_train, y_test = train_test_split(X_cell_train,
                                                                                                      X_drug_train, y_train,
                                                                                                      test_size=0.2,
-                                                                                                     random_state=44,
+                                                                                                     random_state=RANDOM_SEED,
                                                                                                      shuffle=True)
             # Step 9: Train and evaluate the DeepDRA model on the split data
             results = train_DeepDRA(X_cell_train, X_cell_test, X_drug_train, X_drug_test, y_train, y_test, cell_sizes,

utils.py

@@ -7,8 +7,11 @@ RAW_BOTH_DATA_FOLDER = os.path.join(DATA_FOLDER, 'CTRP_GDSC_data')
 DRUG_DATA_FOLDER = os.path.join(DATA_FOLDER, 'drug_data')
 GDSC_RAW_DATA_FOLDER = os.path.join(DATA_FOLDER, 'GDSC_data')
 CCLE_RAW_DATA_FOLDER = os.path.join(DATA_FOLDER, 'CCLE_data')
+CTRP_RAW_DATA_FOLDER = os.path.join(DATA_FOLDER, 'CTRP_data')
+
 GDSC_SCREENING_DATA_FOLDER = os.path.join(GDSC_RAW_DATA_FOLDER, 'drug_screening_matrix_GDSC.tsv')
 CCLE_SCREENING_DATA_FOLDER = os.path.join(CCLE_RAW_DATA_FOLDER, 'drug_screening_matrix_ccle.tsv')
+CTRP_SCREENING_DATA_FOLDER = os.path.join(CTRP_RAW_DATA_FOLDER, 'drug_screening_matrix_ctrp.tsv')
 BOTH_SCREENING_DATA_FOLDER = os.path.join(RAW_BOTH_DATA_FOLDER, 'drug_screening_matrix_gdsc_ctrp.tsv')
 
 CTRP_FOLDER = os.path.join(DATA_FOLDER, 'CTRP')
@@ -27,7 +30,7 @@ SIM_KERNEL = {'cell_CN': ('euclidean', 0.001), 'cell_exp': ('euclidean', 0.01),
 SAVE_MODEL = False  # Change it to True to save the trained model
 VARIATIONAL_AUTOENCODERS = False
 # DATA_MODALITIES=['cell_CN','cell_exp','cell_methy','cell_mut','drug_comp','drug_DT'] # Change this list to only consider specific data modalities
-DATA_MODALITIES = ['cell_mut', 'drug_desc', 'drug_finger']
+DATA_MODALITIES = ['cell_CN','cell_exp','cell_mut', 'drug_desc']
 RANDOM_SEED = 42  # Must be used wherever can be used