Multi layer RNN with LSTM in Tensorflow

I have coded a single layer RNN with LSTM in Tensorflow (ver 1.5) by Python (ver 3.6). I would like to add 3 hidden layers to this RNN (i.e one input layer, one output layer, and three hidden layers). I have read about cell's state, stack, unstack and etc. but I still confuse how to put these things togather and upgrade my code. Below is my code in single layer RNN. Could you please help me to upgrade the code (Note: I am so new to Tensorflow and Python :) ). `

import tensorflow as tf
from tensorflow.contrib import rnn 
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import csv
import sklearn.metrics as sm

inputs = 12            #number of columns input  
num_hidden = 800      #number of neurons in the layer
outputs = 1           #number of columns output  
num_epochs = 100
batch_size = 80
learning_rate = 0.00001

# Training data
input1 = []
output1 = []
with open('train1_leading.csv', 'r') as csv_f:
    data = csv.reader (csv_f) 
    for row in data:
        input1.append (row [0:inputs])
        output1.append (row [inputs])

input11 = []
for i in range(0, len(input1)):
    for j in range(0, inputs):
output1 = [float(x) for x in output1]

input2 = np.array(input11)
output2 = np.array(output1)

x_data = input2[:(len(input2)-(len(input2) % batch_size))]
x_batches = x_data.reshape(-1, batch_size, inputs)   

y_data = output2[:(len(output2)-(len(output2) % batch_size))]
y_batches = y_data.reshape(-1, batch_size, outputs)

# Testing data
inputt = []
outputt = []
with open('valid1_leading.csv', 'r') as csv_f:
    data = csv.reader (csv_f) 
    for row in data:
        inputt.append (row [0:inputs])
        outputt.append (row [inputs])
inputtt = []
for i in range(0, len(inputt)):
    for j in range(0, inputs):
outputt = [float(x) for x in outputt]
inputt1 = np.array(inputtt)
output1 = np.array(outputt)
X_test = inputt1[:batch_size].reshape(-1, batch_size, inputs)
Y_test = output1[-(batch_size):].reshape(-1, batch_size, outputs)

# Configure RNN
tf.reset_default_graph()   #reset graphs

X = tf.placeholder(tf.float32, [None, batch_size, inputs])   #create variables
Y = tf.placeholder(tf.float32, [None, batch_size, outputs])  #create variables

basic_cell = tf.contrib.rnn.BasicRNNCell(num_units=num_hidden,     activation=tf.nn.softsign)   #create RNN object

rnn_output, states = tf.nn.dynamic_rnn(basic_cell, X, dtype=tf.float32)  

stacked_rnn_output = tf.reshape(rnn_output, [-1, num_hidden]) 

weight = tf.Variable(tf.random_normal([num_hidden, outputs]))   
bias = tf.Variable(tf.random_normal([outputs]))   
stacked_outputs = tf.matmul(stacked_rnn_output, weight) + bias  
outputRNN = tf.reshape(stacked_outputs, [-1, batch_size, outputs])              #results

loss = tf.losses.mean_squared_error(outputRNN, Y)   #cost function  
optimizer = tf.train.AdamOptimizer(learning_rate=learning_rate)         
training_op = optimizer.minimize(loss)                                         

with tf.Session() as sess:   #initialize all the variables
    for ep in range(num_epochs):, feed_dict={X: x_batches, Y: y_batches})
        mse = loss.eval(feed_dict={X: x_batches, Y: y_batches})
        print(ep, "\tMSE:", mse)

    y_pred =, feed_dict={X: X_test})

plt.title("Forecast vs Actual", fontsize=14)
plt.plot(pd.Series(np.ravel(Y_test)), "b", markersize=10, label="Actual")
plt.plot(pd.Series(np.ravel(y_pred)), "r", markersize=10, label="Forecast")
plt.legend(loc="upper left")
plt.xlabel("Time Periods")

tt = sm.mean_squared_error(np.ravel(Y_test), np.ravel(y_pred))
print ('MSE of Test data', tt)`  

2 answers

  • answered 2018-02-13 17:50 squadrick

    I've used a three layer LSTM with a dynamic_rnn below, I'm sure you can adopt this use case to whatever is required.

    import tensorflow as tf
    num_layers = 3
    state_size = 100
    init_state = tf.placeholder(tf.float32, [num_layers, 2, None, state_size]) # None is for batch_size
    state_per_layer_list = tf.unstack(init_state, axis=0)
    rnn_tuple_state = tuple(
            for idx in range(num_layers)]
    cell = tf.contrib.rnn.LSTMCell(state_size, state_is_tuple=True)
    cell = tf.contrib.rnn.MultiRNNCell([cell] * num_layers, state_is_tuple=True)
    x = tf.placeholder(tf.float32, [None, None, state_size])
    current_pred, new_states = tf.nn.dynamic_rnn(cell, x, 
    new_states = tf.stack(new_states)

    new_states is Tensor("stack:0", shape=(3, 2, ?, 100), dtype=float32), which can now be feed into the init_state placeholder for the next run.

  • answered 2018-02-13 19:38 major_hart

    Here is code that works for me. Check out for more info on this topic. The dynamic_rnn handles the passing of states and inputs.

        def rnn_cell():
            return tf.contrib.rnn.BasicRNNCell(num_units=num_hidden, activation=tf.nn.softsign)
        self.stacked_rnn = tf.contrib.rnn.MultiRNNCell([rnn_cell() for _ in range(num_layers)])
            final_outputs, final_state = tf.nn.dynamic_rnn(cell=self.stacked_rnn,

    If you want more visibility you can follow the example from the link above

    def lstm_cell():
      return tf.contrib.rnn.BasicLSTMCell(lstm_size)
    stacked_lstm = tf.contrib.rnn.MultiRNNCell(
        [lstm_cell() for _ in range(number_of_layers)])
    initial_state = state = stacked_lstm.zero_state(batch_size, tf.float32)
    for i in range(num_steps):
        # The value of state is updated after processing each batch of words.
        output, state = stacked_lstm(words[:, i], state)
        # The rest of the code.
        # ...
    final_state = state