Training one Autoencoder at a time in a single graph

trainSingle.py

optimizer = tf.train.AdamOptimizer(learning_rate)

with tf.name_scope("phase1"):
    phase1_outputs = tf.matmul(hidden1, weights4) + biases4  # bypass hidden2 and hidden3
    phase1_reconstruction_loss = tf.reduce_mean(tf.square(phase1_outputs - X))
    phase1_reg_loss = regularizer(weights1) + regularizer(weights4)
    phase1_loss = phase1_reconstruction_loss + phase1_reg_loss
    phase1_training_op = optimizer.minimize(phase1_loss)

with tf.name_scope("phase2"):
    phase2_reconstruction_loss = tf.reduce_mean(tf.square(hidden3 - hidden1))
    phase2_reg_loss = regularizer(weights2) + regularizer(weights3)
    phase2_loss = phase2_reconstruction_loss + phase2_reg_loss
    train_vars = [weights2, biases2, weights3, biases3]
    phase2_training_op = optimizer.minimize(phase2_loss, var_list=train_vars) # freeze hidden1