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mhjensen faf9db223a update week 42
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<a class="navbar-brand" href="week42-bs.html">Week 42 Convolutional (CNN) and Recurrent (RNN) Neural Networks</a>
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<!-- navigation toc: --> <li><a href="._week42-bs001.html#___sec0" style="font-size: 80%;">Plan for week 42</a></li>
<!-- navigation toc: --> <li><a href="._week42-bs002.html#___sec1" style="font-size: 80%;">Convolutional Neural Networks (recognizing images)</a></li>
<!-- navigation toc: --> <li><a href="._week42-bs003.html#___sec2" style="font-size: 80%;">Neural Networks vs CNNs</a></li>
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<h2 id="___sec33" class="anchor">Other Types of Recurrent Neural Networks </h2>
<p>
Besides a simple recurrent neural network layer, there are two other
commonly used types of recurrent neural network layers: Long Short
Term Memory (LSTM) and Gated Recurrent Unit (GRU). For a short
introduction to these layers see <a href="https://medium.com/mindboard/lstm-vs-gru-experimental-comparison-955820c21e8b" target="_self"><tt>https://medium.com/mindboard/lstm-vs-gru-experimental-comparison-955820c21e8b</tt></a>
and <a href="https://medium.com/mindboard/lstm-vs-gru-experimental-comparison-955820c21e8b" target="_self"><tt>https://medium.com/mindboard/lstm-vs-gru-experimental-comparison-955820c21e8b</tt></a>.
<p>
The first network created below is similar to the previous network,
but it replaces the SimpleRNN layers with LSTM layers. The second
network below has two hidden layers made up of GRUs, which are
preceeded by two dense (feeddorward) neural network layers. These
dense layers "preprocess" the data before it reaches the recurrent
layers. This architecture has been shown to improve the performance
of recurrent neural networks (see the link above and also
<a href="https://arxiv.org/pdf/1807.02857.pdf" target="_self"><tt>https://arxiv.org/pdf/1807.02857.pdf</tt></a>.
<p>
<!-- code=python (!bc pycod) typeset with pygments style "default" -->
<div class="highlight" style="background: #f8f8f8"><pre style="line-height: 125%"><span></span><span style="color: #008000; font-weight: bold">def</span> <span style="color: #0000FF">lstm_2layers</span>(length_of_sequences, batch_size <span style="color: #666666">=</span> <span style="color: #008000; font-weight: bold">None</span>, stateful <span style="color: #666666">=</span> <span style="color: #008000; font-weight: bold">False</span>):
<span style="color: #BA2121; font-style: italic">&quot;&quot;&quot;</span>
<span style="color: #BA2121; font-style: italic"> Inputs:</span>
<span style="color: #BA2121; font-style: italic"> length_of_sequences (an int): the number of y values in &quot;x data&quot;. This is determined</span>
<span style="color: #BA2121; font-style: italic"> when the data is formatted</span>
<span style="color: #BA2121; font-style: italic"> batch_size (an int): Default value is None. See Keras documentation of SimpleRNN.</span>
<span style="color: #BA2121; font-style: italic"> stateful (a boolean): Default value is False. See Keras documentation of SimpleRNN.</span>
<span style="color: #BA2121; font-style: italic"> Returns:</span>
<span style="color: #BA2121; font-style: italic"> model (a Keras model): The recurrent neural network that is built and compiled by this</span>
<span style="color: #BA2121; font-style: italic"> method</span>
<span style="color: #BA2121; font-style: italic"> Builds and compiles a recurrent neural network with two LSTM hidden layers and returns the model.</span>
<span style="color: #BA2121; font-style: italic"> &quot;&quot;&quot;</span>
<span style="color: #408080; font-style: italic"># Number of neurons on the input/output layer and the number of neurons in the hidden layer</span>
in_out_neurons <span style="color: #666666">=</span> <span style="color: #666666">1</span>
hidden_neurons <span style="color: #666666">=</span> <span style="color: #666666">250</span>
<span style="color: #408080; font-style: italic"># Input Layer</span>
inp <span style="color: #666666">=</span> Input(batch_shape<span style="color: #666666">=</span>(batch_size,
length_of_sequences,
in_out_neurons))
<span style="color: #408080; font-style: italic"># Hidden layers (in this case they are LSTM layers instead if SimpleRNN layers)</span>
rnn<span style="color: #666666">=</span> LSTM(hidden_neurons,
return_sequences<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">True</span>,
stateful <span style="color: #666666">=</span> stateful,
name<span style="color: #666666">=</span><span style="color: #BA2121">&quot;RNN&quot;</span>, use_bias<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">True</span>, activation<span style="color: #666666">=</span><span style="color: #BA2121">&#39;tanh&#39;</span>)(inp)
rnn1 <span style="color: #666666">=</span> LSTM(hidden_neurons,
return_sequences<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">False</span>,
stateful <span style="color: #666666">=</span> stateful,
name<span style="color: #666666">=</span><span style="color: #BA2121">&quot;RNN1&quot;</span>, use_bias<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">True</span>, activation<span style="color: #666666">=</span><span style="color: #BA2121">&#39;tanh&#39;</span>)(rnn)
<span style="color: #408080; font-style: italic"># Output layer</span>
dens <span style="color: #666666">=</span> Dense(in_out_neurons,name<span style="color: #666666">=</span><span style="color: #BA2121">&quot;dense&quot;</span>)(rnn1)
<span style="color: #408080; font-style: italic"># Define the midel</span>
model <span style="color: #666666">=</span> Model(inputs<span style="color: #666666">=</span>[inp],outputs<span style="color: #666666">=</span>[dens])
<span style="color: #408080; font-style: italic"># Compile the model</span>
model<span style="color: #666666">.</span>compile(loss<span style="color: #666666">=</span><span style="color: #BA2121">&#39;mean_squared_error&#39;</span>, optimizer<span style="color: #666666">=</span><span style="color: #BA2121">&#39;adam&#39;</span>)
<span style="color: #408080; font-style: italic"># Return the model</span>
<span style="color: #008000; font-weight: bold">return</span> model
<span style="color: #008000; font-weight: bold">def</span> <span style="color: #0000FF">dnn2_gru2</span>(length_of_sequences, batch_size <span style="color: #666666">=</span> <span style="color: #008000; font-weight: bold">None</span>, stateful <span style="color: #666666">=</span> <span style="color: #008000; font-weight: bold">False</span>):
<span style="color: #BA2121; font-style: italic">&quot;&quot;&quot;</span>
<span style="color: #BA2121; font-style: italic"> Inputs:</span>
<span style="color: #BA2121; font-style: italic"> length_of_sequences (an int): the number of y values in &quot;x data&quot;. This is determined</span>
<span style="color: #BA2121; font-style: italic"> when the data is formatted</span>
<span style="color: #BA2121; font-style: italic"> batch_size (an int): Default value is None. See Keras documentation of SimpleRNN.</span>
<span style="color: #BA2121; font-style: italic"> stateful (a boolean): Default value is False. See Keras documentation of SimpleRNN.</span>
<span style="color: #BA2121; font-style: italic"> Returns:</span>
<span style="color: #BA2121; font-style: italic"> model (a Keras model): The recurrent neural network that is built and compiled by this</span>
<span style="color: #BA2121; font-style: italic"> method</span>
<span style="color: #BA2121; font-style: italic"> Builds and compiles a recurrent neural network with four hidden layers (two dense followed by</span>
<span style="color: #BA2121; font-style: italic"> two GRU layers) and returns the model.</span>
<span style="color: #BA2121; font-style: italic"> &quot;&quot;&quot;</span>
<span style="color: #408080; font-style: italic"># Number of neurons on the input/output layers and hidden layers</span>
in_out_neurons <span style="color: #666666">=</span> <span style="color: #666666">1</span>
hidden_neurons <span style="color: #666666">=</span> <span style="color: #666666">250</span>
<span style="color: #408080; font-style: italic"># Input layer</span>
inp <span style="color: #666666">=</span> Input(batch_shape<span style="color: #666666">=</span>(batch_size,
length_of_sequences,
in_out_neurons))
<span style="color: #408080; font-style: italic"># Hidden Dense (feedforward) layers</span>
dnn <span style="color: #666666">=</span> Dense(hidden_neurons<span style="color: #666666">/2</span>, activation<span style="color: #666666">=</span><span style="color: #BA2121">&#39;relu&#39;</span>, name<span style="color: #666666">=</span><span style="color: #BA2121">&#39;dnn&#39;</span>)(inp)
dnn1 <span style="color: #666666">=</span> Dense(hidden_neurons<span style="color: #666666">/2</span>, activation<span style="color: #666666">=</span><span style="color: #BA2121">&#39;relu&#39;</span>, name<span style="color: #666666">=</span><span style="color: #BA2121">&#39;dnn1&#39;</span>)(dnn)
<span style="color: #408080; font-style: italic"># Hidden GRU layers</span>
rnn1 <span style="color: #666666">=</span> GRU(hidden_neurons,
return_sequences<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">True</span>,
stateful <span style="color: #666666">=</span> stateful,
name<span style="color: #666666">=</span><span style="color: #BA2121">&quot;RNN1&quot;</span>, use_bias<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">True</span>)(dnn1)
rnn <span style="color: #666666">=</span> GRU(hidden_neurons,
return_sequences<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">False</span>,
stateful <span style="color: #666666">=</span> stateful,
name<span style="color: #666666">=</span><span style="color: #BA2121">&quot;RNN&quot;</span>, use_bias<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">True</span>)(rnn1)
<span style="color: #408080; font-style: italic"># Output layer</span>
dens <span style="color: #666666">=</span> Dense(in_out_neurons,name<span style="color: #666666">=</span><span style="color: #BA2121">&quot;dense&quot;</span>)(rnn)
<span style="color: #408080; font-style: italic"># Define the model</span>
model <span style="color: #666666">=</span> Model(inputs<span style="color: #666666">=</span>[inp],outputs<span style="color: #666666">=</span>[dens])
<span style="color: #408080; font-style: italic"># Compile the mdoel</span>
model<span style="color: #666666">.</span>compile(loss<span style="color: #666666">=</span><span style="color: #BA2121">&#39;mean_squared_error&#39;</span>, optimizer<span style="color: #666666">=</span><span style="color: #BA2121">&#39;adam&#39;</span>)
<span style="color: #408080; font-style: italic"># Return the model</span>
<span style="color: #008000; font-weight: bold">return</span> model
<span style="color: #408080; font-style: italic"># Check to make sure the data set is complete</span>
<span style="color: #008000; font-weight: bold">assert</span> <span style="color: #008000">len</span>(X_tot) <span style="color: #666666">==</span> <span style="color: #008000">len</span>(y_tot)
<span style="color: #408080; font-style: italic"># This is the number of points that will be used in as the training data</span>
dim<span style="color: #666666">=12</span>
<span style="color: #408080; font-style: italic"># Separate the training data from the whole data set</span>
X_train <span style="color: #666666">=</span> X_tot[:dim]
y_train <span style="color: #666666">=</span> y_tot[:dim]
<span style="color: #408080; font-style: italic"># Generate the training data for the RNN, using a sequence of 2</span>
rnn_input, rnn_training <span style="color: #666666">=</span> format_data(y_train, <span style="color: #666666">2</span>)
<span style="color: #408080; font-style: italic"># Create a recurrent neural network in Keras and produce a summary of the </span>
<span style="color: #408080; font-style: italic"># machine learning model</span>
<span style="color: #408080; font-style: italic"># Change the method name to reflect which network you want to use</span>
model <span style="color: #666666">=</span> dnn2_gru2(length_of_sequences <span style="color: #666666">=</span> <span style="color: #666666">2</span>)
model<span style="color: #666666">.</span>summary()
<span style="color: #408080; font-style: italic"># Start the timer. Want to time training+testing</span>
start <span style="color: #666666">=</span> timer()
<span style="color: #408080; font-style: italic"># Fit the model using the training data genenerated above using 150 training iterations and a 5%</span>
<span style="color: #408080; font-style: italic"># validation split. Setting verbose to True prints information about each training iteration.</span>
hist <span style="color: #666666">=</span> model<span style="color: #666666">.</span>fit(rnn_input, rnn_training, batch_size<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">None</span>, epochs<span style="color: #666666">=150</span>,
verbose<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">True</span>,validation_split<span style="color: #666666">=0.05</span>)
<span style="color: #408080; font-style: italic"># This section plots the training loss and the validation loss as a function of training iteration.</span>
<span style="color: #408080; font-style: italic"># This is not required for analyzing the couple cluster data but can help determine if the network is</span>
<span style="color: #408080; font-style: italic"># being overtrained.</span>
<span style="color: #008000; font-weight: bold">for</span> label <span style="color: #AA22FF; font-weight: bold">in</span> [<span style="color: #BA2121">&quot;loss&quot;</span>,<span style="color: #BA2121">&quot;val_loss&quot;</span>]:
plt<span style="color: #666666">.</span>plot(hist<span style="color: #666666">.</span>history[label],label<span style="color: #666666">=</span>label)
plt<span style="color: #666666">.</span>ylabel(<span style="color: #BA2121">&quot;loss&quot;</span>)
plt<span style="color: #666666">.</span>xlabel(<span style="color: #BA2121">&quot;epoch&quot;</span>)
plt<span style="color: #666666">.</span>title(<span style="color: #BA2121">&quot;The final validation loss: </span><span style="color: #BB6688; font-weight: bold">{}</span><span style="color: #BA2121">&quot;</span><span style="color: #666666">.</span>format(hist<span style="color: #666666">.</span>history[<span style="color: #BA2121">&quot;val_loss&quot;</span>][<span style="color: #666666">-1</span>]))
plt<span style="color: #666666">.</span>legend()
plt<span style="color: #666666">.</span>show()
<span style="color: #408080; font-style: italic"># Use the trained neural network to predict more points of the data set</span>
test_rnn(X_tot, y_tot, X_tot[<span style="color: #666666">0</span>], X_tot[dim<span style="color: #666666">-1</span>])
<span style="color: #408080; font-style: italic"># Stop the timer and calculate the total time needed.</span>
end <span style="color: #666666">=</span> timer()
<span style="color: #008000">print</span>(<span style="color: #BA2121">&#39;Time: &#39;</span>, end<span style="color: #666666">-</span>start)
<span style="color: #408080; font-style: italic"># ### Training Recurrent Neural Networks in the Standard Way (i.e. learning the relationship between the X and Y data)</span>
<span style="color: #408080; font-style: italic"># </span>
<span style="color: #408080; font-style: italic"># Finally, comparing the performace of a recurrent neural network using the standard data formatting to the performance of the network with time sequence data formatting shows the benefit of this type of data formatting with extrapolation.</span>
<span style="color: #408080; font-style: italic"># Check to make sure the data set is complete</span>
<span style="color: #008000; font-weight: bold">assert</span> <span style="color: #008000">len</span>(X_tot) <span style="color: #666666">==</span> <span style="color: #008000">len</span>(y_tot)
<span style="color: #408080; font-style: italic"># This is the number of points that will be used in as the training data</span>
dim<span style="color: #666666">=12</span>
<span style="color: #408080; font-style: italic"># Separate the training data from the whole data set</span>
X_train <span style="color: #666666">=</span> X_tot[:dim]
y_train <span style="color: #666666">=</span> y_tot[:dim]
<span style="color: #408080; font-style: italic"># Reshape the data for Keras specifications</span>
X_train <span style="color: #666666">=</span> X_train<span style="color: #666666">.</span>reshape((dim, <span style="color: #666666">1</span>))
y_train <span style="color: #666666">=</span> y_train<span style="color: #666666">.</span>reshape((dim, <span style="color: #666666">1</span>))
<span style="color: #408080; font-style: italic"># Create a recurrent neural network in Keras and produce a summary of the </span>
<span style="color: #408080; font-style: italic"># machine learning model</span>
<span style="color: #408080; font-style: italic"># Set the sequence length to 1 for regular data formatting </span>
model <span style="color: #666666">=</span> rnn(length_of_sequences <span style="color: #666666">=</span> <span style="color: #666666">1</span>)
model<span style="color: #666666">.</span>summary()
<span style="color: #408080; font-style: italic"># Start the timer. Want to time training+testing</span>
start <span style="color: #666666">=</span> timer()
<span style="color: #408080; font-style: italic"># Fit the model using the training data genenerated above using 150 training iterations and a 5%</span>
<span style="color: #408080; font-style: italic"># validation split. Setting verbose to True prints information about each training iteration.</span>
hist <span style="color: #666666">=</span> model<span style="color: #666666">.</span>fit(X_train, y_train, batch_size<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">None</span>, epochs<span style="color: #666666">=150</span>,
verbose<span style="color: #666666">=</span><span style="color: #008000; font-weight: bold">True</span>,validation_split<span style="color: #666666">=0.05</span>)
<span style="color: #408080; font-style: italic"># This section plots the training loss and the validation loss as a function of training iteration.</span>
<span style="color: #408080; font-style: italic"># This is not required for analyzing the couple cluster data but can help determine if the network is</span>
<span style="color: #408080; font-style: italic"># being overtrained.</span>
<span style="color: #008000; font-weight: bold">for</span> label <span style="color: #AA22FF; font-weight: bold">in</span> [<span style="color: #BA2121">&quot;loss&quot;</span>,<span style="color: #BA2121">&quot;val_loss&quot;</span>]:
plt<span style="color: #666666">.</span>plot(hist<span style="color: #666666">.</span>history[label],label<span style="color: #666666">=</span>label)
plt<span style="color: #666666">.</span>ylabel(<span style="color: #BA2121">&quot;loss&quot;</span>)
plt<span style="color: #666666">.</span>xlabel(<span style="color: #BA2121">&quot;epoch&quot;</span>)
plt<span style="color: #666666">.</span>title(<span style="color: #BA2121">&quot;The final validation loss: </span><span style="color: #BB6688; font-weight: bold">{}</span><span style="color: #BA2121">&quot;</span><span style="color: #666666">.</span>format(hist<span style="color: #666666">.</span>history[<span style="color: #BA2121">&quot;val_loss&quot;</span>][<span style="color: #666666">-1</span>]))
plt<span style="color: #666666">.</span>legend()
plt<span style="color: #666666">.</span>show()
<span style="color: #408080; font-style: italic"># Use the trained neural network to predict the remaining data points</span>
X_pred <span style="color: #666666">=</span> X_tot[dim:]
X_pred <span style="color: #666666">=</span> X_pred<span style="color: #666666">.</span>reshape((<span style="color: #008000">len</span>(X_pred), <span style="color: #666666">1</span>))
y_model <span style="color: #666666">=</span> model<span style="color: #666666">.</span>predict(X_pred)
y_pred <span style="color: #666666">=</span> np<span style="color: #666666">.</span>concatenate((y_tot[:dim], y_model<span style="color: #666666">.</span>flatten()))
<span style="color: #408080; font-style: italic"># Plot the known data set and the predicted data set. The red box represents the region that was used</span>
<span style="color: #408080; font-style: italic"># for the training data.</span>
fig, ax <span style="color: #666666">=</span> plt<span style="color: #666666">.</span>subplots()
ax<span style="color: #666666">.</span>plot(X_tot, y_tot, label<span style="color: #666666">=</span><span style="color: #BA2121">&quot;true&quot;</span>, linewidth<span style="color: #666666">=3</span>)
ax<span style="color: #666666">.</span>plot(X_tot, y_pred, <span style="color: #BA2121">&#39;g-.&#39;</span>,label<span style="color: #666666">=</span><span style="color: #BA2121">&quot;predicted&quot;</span>, linewidth<span style="color: #666666">=4</span>)
ax<span style="color: #666666">.</span>legend()
<span style="color: #408080; font-style: italic"># Created a red region to represent the points used in the training data.</span>
ax<span style="color: #666666">.</span>axvspan(X_tot[<span style="color: #666666">0</span>], X_tot[dim], alpha<span style="color: #666666">=0.25</span>, color<span style="color: #666666">=</span><span style="color: #BA2121">&#39;red&#39;</span>)
plt<span style="color: #666666">.</span>show()
<span style="color: #408080; font-style: italic"># Stop the timer and calculate the total time needed.</span>
end <span style="color: #666666">=</span> timer()
<span style="color: #008000">print</span>(<span style="color: #BA2121">&#39;Time: &#39;</span>, end<span style="color: #666666">-</span>start)
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