feat: stable

DeepDRA.py

@@ -140,6 +140,8 @@ def train(model, train_loader, val_loader,  num_epochs,class_weights):
 
             # Backward pass and optimization
             total_loss.backward()
+            torch.nn.utils.clip_grad_norm_(model.parameters(), 1)
+
             mlp_optimizer.step()
             total_train_loss += total_loss.item()
 

data_loader.py

@@ -9,7 +9,7 @@ from utils import DRUG_DATA_FOLDER
 
 class RawDataLoader:
     @staticmethod
-    def load_data(data_modalities, raw_file_directory, screen_file_directory, sep):
+    def load_data(data_modalities, raw_file_directory, screen_file_directory, sep, drug_directory=DRUG_DATA_FOLDER):
         """
         Load raw data and screening data, perform intersection, and adjust screening data.
 
@@ -29,7 +29,7 @@ class RawDataLoader:
 
         # Step 2: Load drug data files for specified data modalities
         drug_data = RawDataLoader.load_raw_files(intersect=True, data_modalities=data_modalities,
-                                                 raw_file_directory=DRUG_DATA_FOLDER)
+                                                 raw_file_directory=drug_directory)
 
         # Step 3: Update the 'data' dictionary with drug data
         data.update(drug_data)
@@ -135,14 +135,11 @@ class RawDataLoader:
                 df.columns = df.columns.str.replace('_cell_CN', '')
                 df.columns = df.columns.str.replace('_cell_exp', '')
 
-                # Note that drug_comp raw table has some NA values so we should impute it
-                if any(df.isna()):
-                    df = pd.DataFrame(SimpleImputer(strategy='mean').fit_transform(df),
-                                      columns=df.columns).set_index(df.index)
-                if file.startswith('drug_comp'):  # We need to normalize the drug_data comp dataset
-                    df = ((df - df.mean()) / df.std()).fillna(0)
-                elif file.startswith('drug_desc'):  # We need to normalize the drug_data comp dataset
-                    df = ((df - df.mean()) / df.std()).fillna(0)
+                df = (df - df.min()) / (df.max() - df.min())
+                df = df.fillna(0)
+
+                print("has null:")
+                print(df.isnull().sum().sum())
                 if intersect:
                     if file.startswith('cell'):
                         if cell_line_names:

evaluation.py

@@ -53,7 +53,7 @@ class Evaluation:
 
 
     @staticmethod
-    def evaluate(all_targets, mlp_output, show_plot=True):
+    def evaluate(all_targets, mlp_output, show_plot=False):
         """
         Evaluate model performance based on predictions and targets.
 

main.py

@@ -165,6 +165,7 @@ def run(k, is_test=False ):
                                                             screen_file_directory=GDSC_SCREENING_DATA_FOLDER,
                                                             sep="\t")
 
+
     # Step 3: Load test data if applicable
     if is_test:
         test_data, test_drug_screen = RawDataLoader.load_data(data_modalities=DATA_MODALITIES,
@@ -225,4 +226,4 @@ if __name__ == '__main__':
     torch.manual_seed(RANDOM_SEED)
     random.seed(RANDOM_SEED)
     np.random.seed(RANDOM_SEED)
-    run(10, is_test=False)
+    run(10, is_test=True)

mlp.py

@@ -27,7 +27,7 @@ class MLP(nn.Module):
             nn.Linear(input_dim, 128),
             nn.ReLU(inplace=True),
             nn.Linear(128, output_dim),
-            nn.Hardsigmoid(),
+            nn.Sigmoid(),
         )
 
     def forward(self, x):

utils.py

@@ -8,6 +8,7 @@ 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')
+SIM_DATA_FOLDER = os.path.join(DATA_FOLDER, 'similarity_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')