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multi_view_representation_learning/simple_AE_two_layers.py

+
+"""""""""""""""
+Monomodal Autoenconder  code
+"""""""""""""""
+import keras
+from keras.layers import Input, Dense, concatenate
+from keras.models import Model
+from keras.layers import Dropout
+from keras.callbacks import EarlyStopping
+import matplotlib.pyplot as plt
+plt.switch_backend('agg')
+import sys as os
+import os
+from sklearn.preprocessing import StandardScaler, MinMaxScaler
+from sklearn.decomposition import PCA
+from sklearn.metrics import mean_squared_error
+from math import sqrt
+from keras.optimizers import SGD, Adadelta, Adam
+import numpy as np
+from sklearn.model_selection import KFold
+from keras.callbacks import ModelCheckpoint
+from keras.models import load_model
+
+
+
+
+# loading multimodal fMRI data
+def load_data(sub, view):
+
+    # Import Task fMRI data
+    if view == 1:
+        view_tfmri = np.load(os.path.join(path, "tfmri/{}/gii_matrix_fsaverage5.npy".format(sub)))
+        return view_tfmri
+
+    # Import Resting-State fMRI data
+    if view == 2:
+        view_rsfmri = np.load(os.path.join(path, "rsfmri/{}/correlation_matrix_fsaverage5.npy".format(sub)))
+        return view_rsfmri
+
+    # Import concatenated fMRI data
+    if view ==3:
+        view_rsfmri = np.load(os.path.join(path, "rsfmri/{}/correlation_matrix_fsaverage5.npy".format(sub)))
+        view_tfmri = np.load(os.path.join(path, "tfmri/{}/gii_matrix_fsaverage5.npy".format(sub)))
+        fmri_data =np.concatenate([view_tfmri, view_rsfmri], axis=1)
+        return fmri_data
+
+
+
+
+
+# Path
+path = "/home/asellami/data_fsaverage5"
+
+print('View 1: task-fMRI')
+print('View 2: resting-state fMRI')
+print('View=3: concatenated views (task-fMRI + rest-fMRI)')
+
+# view =1: tfmri, view =2: rsfmri, view=3: concatenated views (task-fMRI + rest-fMRI)
+view=1
+
+# activation functions
+hidden_layer='linear'
+output_layer='linear'
+
+# MSE
+mse_train = []
+mse_test = []
+# RMSE
+rmse_train = []
+rmse_test = []
+#
+# Standard deviation MSE
+std_mse_train = []
+std_mse_test = []
+# Standard deviation RMSE
+std_rmse_train = []
+std_rmse_test = []
+# missing data
+missing_data=[36]
+index_subjects=np.arange(3,43)
+index_subjects = np.delete(index_subjects, np.argwhere(index_subjects == missing_data))
+
+#ar = np.arange(75,101)
+#dimensions = ar[ar%2==0]
+
+dimensions=[2, 6, 10, 16, 20, 26, 30, 36, 40, 46, 50, 56, 60, 66, 70, 76, 80, 86, 90, 96, 100]
+batch_1=dimensions[0:6]
+batch_2=dimensions[6:12]
+batch_3=dimensions[12:17]
+batch_4=dimensions[17:21]
+for dim in batch_1:
+    # create directory
+    directory = '{}'.format(dim)
+    if not os.path.exists(directory):
+        os.makedirs(directory)
+    # Cross Validation
+    kf = KFold(n_splits=10)
+    print(kf.get_n_splits(index_subjects))
+    print("number of splits:", kf)
+    print("number of features:", dimensions)
+    cvscores_mse_test = []
+    cvscores_rmse_test = []
+    cvscores_mse_train = []
+    cvscores_rmse_train = []
+    fold = 0
+    for train_index, test_index in kf.split(index_subjects):
+        fold += 1
+        # create directory
+        directory = '{}/fold_{}'.format(dim, fold)
+        if not os.path.exists(directory):
+            os.makedirs(directory)
+        print(f"Fold #{fold}")
+        print("TRAIN:", index_subjects[train_index], "TEST:", index_subjects[test_index])
+        # load training and testing data
+        print('Load training data... (view {})'.format(view))
+        train_data = np.concatenate([load_data(sub, view) for sub in index_subjects[train_index]])
+        print("Shape of the training data:", train_data.shape)
+        print('Load testdata... (view {})'.format(view))
+        test_data = np.concatenate([load_data(sub, view) for sub in index_subjects[test_index]])
+        print("Shape of the test data:", test_data.shape)
+        # Data normalization to range [-1, 1]
+        print("Data normalization to range [0, 1]")
+        scaler = MinMaxScaler()
+        normalized_train_data = scaler.fit_transform(train_data)
+        normalized_test_data = scaler.fit_transform(test_data)
+
+        # Apply linear autoencoder
+        # Inputs Shape
+        input_train_data = Input(shape=(normalized_train_data[0].shape))
+        # Create linear AE
+        encoded = Dense(110, activation=hidden_layer)(input_train_data)
+        encoded = Dense(dim, activation=hidden_layer)(encoded)
+        decoded = Dense(110, activation=hidden_layer)(encoded)
+        decoded = Dense(normalized_train_data[0].shape[0], activation=output_layer)(decoded)
+        # This model maps an input to its reconstruction
+        autoencoder = Model(input_train_data, decoded)
+        adam= Adam(lr=0.001, beta_1=0.9, beta_2=0.999, amsgrad=False)
+        autoencoder.compile(optimizer=adam, loss='mse')
+        print(autoencoder.summary())
+        # fit Autoencoder on training set
+        history = autoencoder.fit(normalized_train_data, normalized_train_data,
+                                  epochs=70,
+                                  batch_size=1000,
+                                  shuffle=True,
+                                  validation_data=(normalized_test_data, normalized_test_data), verbose=1)
+        # list all data in history
+        print(history.history.keys())
+        # use our encoded layer to encode the training input
+        encoder = Model(input_train_data, encoded)
+        #  create a placeholder for an encoded (32-dimensional) input
+        encoded_input = Input(shape=(dim,))
+        # retrieve the last layer of the autoencoder model
+        decoder_layer_1 = autoencoder.layers[-2]
+        decoder_layer_2 = autoencoder.layers[-1]
+        # create the decoder model
+        decoder = Model(encoded_input, decoder_layer_2(decoder_layer_1(encoded_input)))
+
+        # save models
+        autoencoder.save('{}/fold_{}/autoencoder.h5'.format(dim, fold))
+        encoder.save('{}/fold_{}/encoder.h5'.format(dim, fold))
+        decoder.save('{}/fold_{}/decoder.h5'.format(dim, fold))
+
+        # plot our loss
+        plt.plot(history.history['loss'], label='loss_fold_{}'.format(fold))
+        plt.plot(history.history['val_loss'], label='val_loss_fold_{}'.format(fold))
+        print("vector of val_loss", history.history['val_loss'])
+        plt.title('model train vs validation loss')
+        plt.ylabel('loss')
+        plt.xlabel('epoch')
+        plt.legend()
+        plt.savefig('{}/fold_{}/loss.png'.format(dim, fold))
+        plt.savefig('{}/fold_{}/loss.pdf'.format(dim, fold))
+        plt.close()
+
+        # Apply the mapping (transform) to both the training set and the test set
+        X_train_AE = encoder.predict(normalized_train_data)
+        X_test_AE = encoder.predict(normalized_test_data)
+
+        print("Original shape:   ", normalized_train_data.shape)
+        print("Transformed shape:", X_train_AE.shape)
+
+        # Reconstruction of training data
+        print("Reconstruction of training data... ")
+        X_train_new = autoencoder.predict(normalized_train_data)
+        print("Max value of predicted training data", np.max(X_train_new))
+        print("Min value of predicted training data", np.min(X_train_new))
+        print("Reconstructed matrix shape:", X_train_new.shape)
+        val_mse_train = mean_squared_error(normalized_train_data, X_train_new)
+        print('Value of MSE (train) : ', val_mse_train)
+        cvscores_mse_train.append(val_mse_train)
+        val_rmse = sqrt(val_mse_train)
+        print('Value of RMSE (train)  : ', val_rmse)
+        cvscores_rmse_train.append(val_rmse)
+        # Reconstruction of test data
+        print("Reconstruction of test data... ")
+        X_test_new = autoencoder.predict(normalized_test_data)
+        print("Max value of predicted test data", np.max(X_test_new))
+        print("Min value of predicted test data", np.min(X_test_new))
+        print("Reconstructed matrix shape:", X_test_new.shape)
+        val_mse = mean_squared_error(normalized_test_data, X_test_new)
+        cvscores_mse_test.append(val_mse)
+        print('Value of MSE (test) : ', val_mse)
+        val_rmse = sqrt(val_mse)
+        print('Value of MSE (test) : ', val_rmse)
+        cvscores_rmse_test.append(val_rmse)
+        # transform and save latent representation
+
+
+    print("shape of  mse vector (train):", np.array([cvscores_mse_train]).shape)
+    print(cvscores_mse_train)
+    np.save('{}/cvscores_mse_train.npy'.format(dim), np.array([cvscores_mse_train]))
+    print("shape of  mse vector(test):", np.array([cvscores_mse_test]).shape)
+    print(cvscores_mse_test)
+    np.save('{}/cvscores_mse_test.npy'.format(dim), np.array([cvscores_mse_test]))
+    print("shape of rmse vector (train):", np.array([cvscores_rmse_train]).shape)
+    print(cvscores_rmse_train)
+    np.save('{}/cvscores_rmse_train.npy'.format(dim), np.array([cvscores_rmse_train]))
+    print("shape of rmse vector (test):", np.array([cvscores_rmse_test]).shape)
+    print(cvscores_rmse_test)
+    np.save('{}/cvscores_rmse_test.npy'.format(dim), np.array([cvscores_rmse_test]))
+    print("%.3f%% (+/- %.5f%%)" % (np.mean(cvscores_mse_test), np.std(cvscores_mse_test)))
+    mse_train.append(np.mean(cvscores_mse_train))
+    std_mse_train.append(np.std(cvscores_mse_train))
+    mse_test.append(np.mean(cvscores_mse_test))
+    std_mse_test.append(np.std(cvscores_mse_test))
+    rmse_train.append(np.mean(cvscores_rmse_train))
+    std_rmse_train.append(np.std(cvscores_rmse_train))
+    rmse_test.append(np.mean(cvscores_rmse_test))
+    std_rmse_test.append(np.std(cvscores_rmse_test))
+
+# save MSE, RMSE, and STD vectors for training and test sets
+np.save('mse_train_mean.npy', np.array([mse_train]))
+np.save('rmse_train_mean.npy', np.array([rmse_train]))
+np.save('std_mse_train_mean.npy', np.array([std_mse_train]))
+np.save('std_rmse_train_mean.npy', np.array([std_rmse_train]))
+
+np.save('mse_test_mean.npy', np.array([mse_test]))
+np.save('rmse_test_mean.npy', np.array([rmse_test]))
+np.save('std_mse_test_mean.npy', np.array([std_mse_test]))
+np.save('std_rmse_test_mean.npy', np.array([std_rmse_test]))
+# plotting the mse train
+# setting x and y axis range
+# plotting the mse train
+plt.plot(dimensions, mse_train, label="mse_train")
+plt.plot(dimensions, mse_test, label="mse_test")
+plt.xlabel('Encoding dimension')
+plt.ylabel('Reconstruction error (MSE)')
+# showing legend
+plt.legend()
+plt.savefig('reconstruction_error_mse.pdf')
+plt.savefig('reconstruction_error_mse.png')
+plt.close()
+# plotting the rmse train
+# setting x and y axis range
+plt.plot(dimensions, rmse_train, label="rmse_train")
+plt.plot(dimensions, rmse_test, label="rmse_test")
+plt.xlabel('Encoding dimension')
+plt.ylabel('Reconstruction error (RMSE)')
+# showing legend
+plt.legend()
+plt.savefig('reconstruction_error_rmse.pdf')
+plt.savefig('reconstruction_error_rmse.png')
+plt.close()
+