feat: add main files

DeepDRA.py

@@ -5,7 +5,7 @@ from torch.optim import lr_scheduler
 from autoencoder import Autoencoder
 from evaluation import Evaluation
 from mlp import MLP
-from utils import *
+from utils import MODEL_FOLDER
 
 
 class DeepDRA(nn.Module):
@@ -162,10 +162,6 @@ def test(model, test_loader, reverse=False):
         # Apply reverse if specified
         predictions = 1 - mlp_output if reverse else mlp_output
 
-        # # Store predictions and ground truth labels
-        # all_predictions.extend(predictions.cpu().numpy())
-        # all_labels.extend(labels.cpu().numpy())
-
     # Evaluate the predictions using the specified metrics
     result = Evaluation.evaluate(labels, predictions)
 

data_loader.py

@@ -1,6 +1,11 @@
-from utils import *
+import pandas as pd
+import numpy as np
+from tqdm import tqdm
+from sklearn.impute import SimpleImputer
 import os
 
+from utils import DRUG_DATA_FOLDER
+
 
 class RawDataLoader:
     @staticmethod
@@ -39,7 +44,6 @@ class RawDataLoader:
         # Step 5: Return the loaded data and adjusted drug screening data
         return data, drug_screen
 
-
     @staticmethod
     def intersect_features(data1, data2):
         """
@@ -109,7 +113,6 @@ class RawDataLoader:
 
         return data[0]
 
-
     @staticmethod
     def load_raw_files(raw_file_directory, data_modalities, intersect=True):
         raw_dict = {}
@@ -132,8 +135,6 @@ 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),
@@ -168,13 +169,12 @@ class RawDataLoader:
     @staticmethod
     def load_screening_files(filename="AUC_matS_comb.tsv", sep=',', ):
         df = pd.read_csv(filename, sep=sep, index_col=0)
-        # df = df.drop(['Erlotinib','17-AAG','PD-0325901','PHA-665752','PHA-665752','TAE684','Sorafenib','PLX4720','selumetinib','PD-0332991','Paclitaxel','Nilotinib','Saracatinib'],axis=1)
         return df
-        # return pd.read_csv(os.path.join(DATA_FOLDER, "drug_screening_matrix_GDSC.tsv"), sep='\t', index_col=0)
 
     @staticmethod
     def adjust_screening_raw(drug_screen, data_dict):
         raw_cell_names = []
+        raw_drug_names = []
         for key, value in data_dict.items():
             if 'cell' in key:
                 if len(raw_cell_names) == 0:
@@ -187,7 +187,6 @@ class RawDataLoader:
         screening_cell_names = drug_screen.index
         screening_drug_names = drug_screen.columns
 
-
         common_cell_names = list(set(raw_cell_names).intersection(set(screening_cell_names)))
         common_drug_names = list(set(raw_drug_names).intersection(set(screening_drug_names)))
         for key, value in data_dict.items():

evaluation.py

@@ -1,66 +1,102 @@
 from sklearn.metrics import roc_auc_score, average_precision_score, confusion_matrix, f1_score, precision_score, \
     recall_score, accuracy_score
+from matplotlib import pyplot as plt
+from sklearn import metrics
+import numpy as np
+import pandas as pd
+from statsmodels.stats.weightstats import ttest_ind
 
-from utils import *
 
 
 class Evaluation:
     @staticmethod
     def plot_train_val_accuracy(train_accuracies, val_accuracies, num_epochs):
-        plt.xlabel('epoch')
-        plt.ylabel('accuracy')
-        plt.title('h')
-        plt.plot(range(1, num_epochs + 1), train_accuracies)
-        plt.plot(range(1, num_epochs + 1), val_accuracies)
+        """
+        Plot training and validation accuracies over epochs.
+
+        Parameters:
+        - train_accuracies (list): List of training accuracies.
+        - val_accuracies (list): List of validation accuracies.
+        - num_epochs (int): Number of training epochs.
+
+        Returns:
+        - None
+        """
+        plt.xlabel('Epoch')
+        plt.ylabel('Accuracy')
+        plt.title('Training and Validation Accuracies')
+        plt.plot(range(1, num_epochs + 1), train_accuracies, label='Train Accuracy')
+        plt.plot(range(1, num_epochs + 1), val_accuracies, label='Validation Accuracy')
+        plt.legend()
         plt.show()
 
     @staticmethod
     def plot_train_val_loss(train_loss, val_loss, num_epochs):
-        plt.xlabel('epoch')
-        plt.ylabel('loss')
-        plt.title('h')
-        plt.plot(range(1, num_epochs + 1), train_loss)
-        plt.plot(range(1, num_epochs + 1), val_loss)
+        """
+        Plot training and validation losses over epochs.
+
+        Parameters:
+        - train_loss (list): List of training losses.
+        - val_loss (list): List of validation losses.
+        - num_epochs (int): Number of training epochs.
+
+        Returns:
+        - None
+        """
+        plt.xlabel('Epoch')
+        plt.ylabel('Loss')
+        plt.title('Training and Validation Losses')
+        plt.plot(range(1, num_epochs + 1), train_loss, label='Train Loss')
+        plt.plot(range(1, num_epochs + 1), val_loss, label='Validation Loss')
+        plt.legend()
         plt.show()
 
+
     @staticmethod
     def evaluate(all_targets, mlp_output, show_plot=True):
+        """
+        Evaluate model performance based on predictions and targets.
+
+        Parameters:
+        - all_targets (numpy.ndarray): True target labels.
+        - mlp_output (numpy.ndarray): Predicted probabilities.
+        - show_plot (bool): Whether to display ROC and PR curves.
+
+        Returns:
+        - results (dict): Dictionary containing evaluation metrics.
+        """
+        # Step 1: Convert predicted probabilities to binary labels
         predicted_labels = np.where(mlp_output > 0.5, 1, 0)
-        # Collect predictions and targets for later evaluation
         predicted_labels = predicted_labels.reshape(-1)
-        # Convert predictions and targets to numpy arrays
         all_predictions = predicted_labels
 
-        # Calculate and print AUC
+        # Step 2: Calculate and print AUC
         fpr, tpr, thresholds = metrics.roc_curve(all_targets, mlp_output)
         auc = np.round(metrics.auc(fpr, tpr), 2)
 
-        # Calculate and print AUPRC
-        print(all_targets)
+        # 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 = average_precision_score(all_targets, mlp_output)
-
-        print('Accuracy: {:.2f}'.format(np.round(accuracy_score(all_targets, all_predictions), 2)))
-        print('AUC: {:.2f}'.format(auc))
-        print('AUPRC: {:.2f}'.format(auprc))
 
-        # Calculate and print confusion matrix
+        # Step 4: Print accuracy, AUC, AUPRC, and confusion matrix
+        accuracy = accuracy_score(all_targets, all_predictions)
         cm = confusion_matrix(all_targets, all_predictions)
-        accuracy = cm.trace() / np.sum(cm)
         precision = cm[0, 0] / (cm[0, 0] + cm[0, 1])
         recall = cm[0, 0] / (cm[0, 0] + cm[1, 0])
         f1_score = 2 * precision * recall / (precision + recall)
-        print('Confusion matrix:\n', cm, sep='')
-        print(f'Accuracy: {accuracy:.3f}, Precision: {precision:.3f}, Recall: {recall:.3f}, F1 score: {f1_score:.3f}')
+        print(f'Accuracy: {accuracy:.2f}')
+        print(f'AUC: {auc:.2f}')
+        print(f'AUPRC: {auprc:.2f}')
+        print(f'Confusion matrix:\n{cm}')
+        print(f'Precision: {precision:.3f}, Recall: {recall:.3f}, F1 score: {f1_score:.3f}')
 
+        # Step 5: Display ROC and PR curves if requested
         if show_plot:
             plt.xlabel('False Positive Rate')
             plt.ylabel('True Positive Rate')
             plt.title(f'ROC Curve: AUC={auc}')
             plt.plot(fpr, tpr)
             plt.show()
-            # print(f'AUC: {auc}')
 
             plt.xlabel('Recall')
             plt.ylabel('Precision')
@@ -68,6 +104,7 @@ class Evaluation:
             plt.plot(recall, precision)
             plt.show()
 
+            # Violin plot for DeepDRA scores
             prediction_targets = pd.DataFrame({}, columns=['Prediction', 'Target'])
 
             res = pd.concat(
@@ -76,11 +113,8 @@ class Evaluation:
 
             res.columns = prediction_targets.columns
             prediction_targets = pd.concat([prediction_targets, res])
-
-            class_one = prediction_targets.loc[prediction_targets['Target'] == 0, 'Prediction'].astype(
-                np.float32).tolist()
-            class_minus_one = prediction_targets.loc[prediction_targets['Target'] == 1, 'Prediction'].astype(
-                np.float32).tolist()
+            class_one = prediction_targets.loc[prediction_targets['Target'] == 0, 'Prediction']
+            class_minus_one = prediction_targets.loc[prediction_targets['Target'] == 1, 'Prediction']
 
             fig, ax = plt.subplots()
             ax.set_ylabel("DeepDRA score")
@@ -92,12 +126,13 @@ class Evaluation:
             p_value = np.format_float_scientific(ttest_ind(class_one, class_minus_one)[1])
             cancer = 'all'
             plt.title(
-                f'Responder/Non responder scores for {cancer} cancer with \np-value ~= {p_value[0]}e{p_value[-3:]} ')
+                f'Responder/Non-responder scores for {cancer} cancer with \np-value ~= {p_value[0]}e{p_value[-3:]} ')
             bp = ax.violinplot(data_to_plot, showextrema=True, showmeans=True, showmedians=True)
             bp['cmeans'].set_color('r')
             bp['cmedians'].set_color('g')
             plt.show()
 
+        # Step 6: Return evaluation metrics in a dictionary
         return {'Accuracy': accuracy, 'Precision': precision, 'Recall': recall, 'F1 score': f1_score, 'AUC': auc,
                 'AUPRC': auprc}
 

main.py

@@ -7,10 +7,10 @@ from DeepDRA import DeepDRA, train, test
 from data_loader import RawDataLoader
 from evaluation import Evaluation
 from utils import *
-from mlp import MLP
 import random
 import torch
 import numpy as np
+import pandas as pd
 
 
 def train_DeepDRA(x_cell_train, x_cell_test, x_drug_train, x_drug_test, y_train, y_test, cell_sizes, drug_sizes):
@@ -60,10 +60,10 @@ def train_DeepDRA(x_cell_train, x_cell_test, x_drug_train, x_drug_test, y_train,
     train(model, train_loader, num_epochs=num_epochs)
 
     # Step 7: Save the trained model
-    torch.save(model, 'DeepDRA.pth')
+    torch.save(model,  MODEL_FOLDER + 'DeepDRA.pth')
 
     # Step 8: Load the saved model
-    model = torch.load('DeepDRA.pth')
+    model = torch.load( MODEL_FOLDER + 'DeepDRA.pth')
 
     # Step 9: Convert your test data to PyTorch tensors
     x_cell_test_tensor = torch.Tensor(x_cell_test.values)

mlp.py

@@ -2,7 +2,6 @@ from torch import nn
 from torch import optim, no_grad
 import torch
 from evaluation import Evaluation
-from utils import data_modalities_abbreviation
 class EarlyStopper:
     def __init__(self, patience=1, min_delta=0):
         self.patience = patience

utils.py

@@ -1,40 +1,15 @@
 import os
-import pandas as pd
-import numpy as np
-from tqdm import tqdm
-import sklearn as sk
-from matplotlib import pyplot as plt
-from scipy.spatial.distance import pdist, squareform
-import h2o
-from h2o.estimators import H2ODeepLearningEstimator
-from sklearn.impute import SimpleImputer
-import torch
-import torch.nn as nn
-import torch.optim as optim
-from torch.utils.data import DataLoader, TensorDataset
-import pickle
-from sklearn import metrics
-from copy import deepcopy
-import pyreadr
-import requests
-from time import time
-from math import ceil
-from statsmodels.stats.weightstats import ttest_ind
-import torch.optim.lr_scheduler as lr_scheduler
-from sklearn.model_selection import KFold
+
 
 DATA_FOLDER = 'data'
-RES_DATA_FOLDER = os.path.join(DATA_FOLDER, 'res')
-TEST_DATA_FOLDER = os.path.join(DATA_FOLDER, 'final_test_data')
 TEST_TCGA_DATA_FOLDER = os.path.join(DATA_FOLDER, 'TCGA_test_data')
-SIM_DATA_FOLDER = os.path.join(DATA_FOLDER, 'similarity_data')
-RAW_DATA_FOLDER = os.path.join(DATA_FOLDER, 'raw_data')
-RAW_BOTH_DATA_FOLDER = os.path.join(DATA_FOLDER, 'CTRP_GDSC_Data')
+RAW_BOTH_DATA_FOLDER = os.path.join(DATA_FOLDER, 'CTRP_GDSC_data')
 DRUG_DATA_FOLDER = os.path.join(DATA_FOLDER, 'drug_data')
-
-NEW_RAW_DATA_FOLDER = os.path.join(DATA_FOLDER, 'new_raw_data')
 GDSC_RAW_DATA_FOLDER = os.path.join(DATA_FOLDER, 'GDSC_data')
-CCLE_RAW_DATA_FOLDER = os.path.join(DATA_FOLDER, 'CCLE_raw')
+CCLE_RAW_DATA_FOLDER = os.path.join(DATA_FOLDER, 'CCLE_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')
+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')
 GDSC_FOLDER = os.path.join(DATA_FOLDER, 'GDSC')
@@ -42,32 +17,7 @@ CCLE_FOLDER = os.path.join(DATA_FOLDER, 'CCLE')
 
 MODEL_FOLDER = os.path.join(DATA_FOLDER, 'model')
 
-CTRP_EXPERIMENT_FILE = os.path.join(CTRP_FOLDER, 'v20.meta.per_experiment.txt')
-CTRP_COMPOUND_FILE = os.path.join(CTRP_FOLDER, 'v20.meta.per_compound.txt')
-CTRP_CELLLINE_FILE = os.path.join(CTRP_FOLDER, 'v20.meta.per_cell_line.txt')
-CTRP_AUC_FILE = os.path.join(CTRP_FOLDER, 'v20.data.curves_post_qc.txt')
-
-GDSC_AUC_FILE = os.path.join(GDSC_FOLDER, 'GDSC2_fitted_dose_response.csv')
-GDSC_cnv_data_FILE = os.path.join(GDSC_FOLDER, 'cnv_abs_copy_number_picnic_20191101.csv')
-GDSC_methy_data_FILE = os.path.join(GDSC_FOLDER, 'F2_METH_CELL_DATA.txt')
-GDSC_methy_sampleIds_FILE = os.path.join(GDSC_FOLDER, 'methSampleId_2_cosmicIds.xlsx')
-GDSC_exp_data_FILE = os.path.join(GDSC_FOLDER, 'Cell_line_RMA_proc_basalExp.txt')
-GDSC_exp_sampleIds_FILE = os.path.join(GDSC_FOLDER, 'E-MTAB-3610.sdrf.txt')
-GDSC_mut_data_FILE = os.path.join(GDSC_FOLDER, 'mutations_all_20230202.csv')
-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')
-BOTH_SCREENING_DATA_FOLDER = os.path.join(RAW_BOTH_DATA_FOLDER, 'drug_screening_matrix_gdsc_ctrp.tsv')
-
-CCLE_mut_data_FILE = os.path.join(CCLE_FOLDER, 'CCLE_mutations.csv')
-
-TABLE_RESULTS_FILE = os.path.join(DATA_FOLDER, 'drug_screening_table.tsv')
-MATRIX_RESULTS_FILE = os.path.join(DATA_FOLDER, 'drug_screening_matrix.tsv')
-
-MODEL_FILE = os.path.join(MODEL_FOLDER, 'trained_model_V1_EMDP.sav')
-TEST_FILE = os.path.join(TEST_DATA_FOLDER, 'test.gzip')
-RESULT_FILE = os.path.join(RES_DATA_FOLDER, 'result.tsv')
-
-TCGA_DATA_FOLDER = os.path.join(DATA_FOLDER, 'TCGA_test_data')
+TCGA_DATA_FOLDER = os.path.join(DATA_FOLDER, 'TCGA_data')
 TCGA_SCREENING_DATA = os.path.join(TCGA_DATA_FOLDER, 'TCGA_screening_matrix.tsv')
 
 BUILD_SIM_MATRICES = True  # Make this variable True to build similarity matrices from raw data
@@ -81,36 +31,4 @@ DATA_MODALITIES = ['cell_mut', 'drug_desc', 'drug_finger']
 RANDOM_SEED = 42  # Must be used wherever can be used
 
 
-def data_modalities_abbreviation():
-    abb = []
-    if 'cell_CN' in DATA_MODALITIES:
-        abb.append('C')
-    if 'cell_exp' in DATA_MODALITIES:
-        abb.append('E')
-    if 'cell_mut' in DATA_MODALITIES:
-        abb.append('M')
-    if 'cell_methy' in DATA_MODALITIES:
-        abb.append('T')
-    if 'drug_DT' in DATA_MODALITIES:
-        abb.append('D')
-    if 'drug_comp' in DATA_MODALITIES:
-        abb.append('P')
-    return ''.join(abb)
-
-
-""" TRAIN_INTEGRATION_METHOD used for each cell's and drug_data's data definitions: 
-SIMILARITY: A kernel based integration method in which based on the similarity of each cell's data with the training cell's
-data the input features for the multi layer perceptron (MLP) is constructed. The similarity function used could be different for
-each data modality (euclidean, jaccard,l1_norm, or ...)
-
-AUTO_ENCODER_V1: In this version of integrating multi-omics, for each data modality an autoencoder is trained to reduce the
-dimension of the features and finally a concatenation of each autoencoder's latent space builds up the input layer of the MLP.
-
-AUTO_ENCODER_V2: In this version of integrating multi-omics data, we train a big autoencoder which reduces the dimension of 
-all the different data modalities features at the same time to a smaller feature space. This version of integrating could
-take a lot of memory and time to integrate the data and might be computationally expensive.
 
-AUTO_ENCODER_V3: IN this version of integrating multi-omics data, we train an autoencoder for all the modalities kinda same as 
-the autoencoder version 2 but with this difference that the encoder and decoder layers are separate from each other and 
-just the latent layer is shared among different data modalities.
-"""