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import autoreg
import GPy
import numpy as np
from matplotlib import pyplot as plt
from __future__ import print_function
%matplotlib inline
from autoreg.benchmark import tasks
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# Function to compute root mean square error:
def comp_RMSE(a,b):
return np.sqrt(np.square(a.flatten()-b.flatten()).mean())
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# Define class for normalization
class Normalize(object):
def __init__(self, data, name, norm_name):
self.data_mean = data.mean(axis=0)
self.data_std = data.std(axis=0)
self.normalization_computed = True
setattr(self, name, data)
setattr(self, norm_name, (data-self.data_mean) / self.data_std )
def normalize(self, data, name, norm_name):
if hasattr(self,norm_name):
raise ValueError("This normalization name already exist, choose another one")
setattr(self, name, data )
setattr(self, norm_name, (data-self.data_mean) / self.data_std )
def denormalize(self, data):
return data*self.data_std + self.data_mean
In [16]:
trainned_models_folder_name = "/Users/grigoral/work/code/RGP/examples/identif_trainded"
task_name = 'IdentificationExample5'
# task names:
# Actuator, Ballbeam, Drive, Gas_furnace, Flutter, Dryer, Tank,
# IdentificationExample1..5
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task = getattr( tasks, task_name)
task = task()
task.load_data()
print("Data OUT train shape: ", task.data_out_train.shape)
print("Data IN train shape: ", task.data_in_train.shape)
print("Data OUT test shape: ", task.data_out_test.shape)
print("Data IN test shape: ", task.data_in_test.shape)
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normalize = False
in_data = Normalize(task.data_in_train,'in_train','in_train_norm' )
out_data = Normalize(task.data_out_train,'out_train','out_train_norm' )
in_data.normalize(task.data_in_test, 'in_test','in_test_norm')
out_data.normalize(task.data_out_test, 'out_test','out_test_norm')
if normalize:
out_train = out_data.out_train_norm #out_data.out_train
in_train = in_data.in_train_norm # in_data.in_train
out_test = out_data.out_test_norm #out_data.out_test
in_test = in_data.in_test_norm #in_data.in_test
else:
out_train = out_data.out_train #out_data.out_train
in_train = in_data.in_train # in_data.in_train
out_test = out_data.out_test #out_data.out_test
in_test = in_data.in_test #in_data.in_test
print("Training OUT mean: ", out_train.mean(0));
print("Training OUT std: ", out_train.std(0))
print("")
print("Test OUT mean: ", out_test.mean(0));
print("Test OUT std: ", out_test.std(0))
print("")
print("Training IN mean: ", in_train.mean(0));
print("Training IN std: ", in_train.std(0))
print("")
print("Test IN mean: ", in_test.mean(0));
print("Test IN std: ", in_test.std(0))
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# Plot training:
fig1 = plt.figure(1,figsize=(20,8))
fig1.suptitle('Training data')
ax1 = plt.subplot(1,2,1)
ax1.plot(out_train)
ax1.set_title('Data OUT training')
ax2 = plt.subplot(1,2,2)
ax2.plot(in_train)
ax2.set_title('Data IN training')
fig2 = plt.figure(2,figsize=(20,8))
fig2.suptitle('Test data')
ax3 = plt.subplot(1,2,1)
ax3.plot(out_test)
ax3.set_title('Data OUT test')
ax4 = plt.subplot(1,2,2)
ax4.plot(in_test)
ax4.set_title('Data IN test')
del ax1, ax2, ax3, ax4
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Q = 50 # 200 # Inducing points num
win_in = task.win_in # 20
win_out = task.win_out # 20
use_controls = True
back_cstr = False
inference_method = None
# 1 layer:
wins = [0, win_out] # 0-th is output layer
nDims = [out_train.shape[1],1]
# 2 layers:
# wins = [0, win_out, win_out]
# nDims = [out_train.shape[1],1,1]
MLP_dims = [300,200]
print("Input window: ", win_in)
print("Output window: ", win_out)
m = autoreg.DeepAutoreg(wins, out_train, U=in_train, U_win=win_in,
num_inducing=Q, back_cstr=back_cstr, MLP_dims=MLP_dims, nDims=nDims,
init='Y', # how to initialize hidden states means
X_variance=0.05, # how to initialize hidden states variances
#inference_method=inference_method, # Inference method
# 1 layer:
kernels=[GPy.kern.RBF(win_out,ARD=True,inv_l=True),
GPy.kern.RBF(win_in + win_out,ARD=True,inv_l=True)] )
# 2 layers:
# kernels=[GPy.kern.RBF(win_out,ARD=True,inv_l=True),
# GPy.kern.RBF(win_out+win_out,ARD=True,inv_l=True),
# GPy.kern.RBF(win_out+win_in,ARD=True,inv_l=True)])
#m = autoreg.DeepAutoreg([0,win_out],out_train, U=in_train, U_win=win_in,X_variance=0.01,
# num_inducing=50)
# pattern for model name: #task_name, inf_meth=?, wins=layers, Q = ?, backcstr=?,MLP_dims=?, nDims=
model_file_name = '%s--inf_meth=%s--wins=%s--Q=%i--backcstr=%i--nDims=%s' % (task.name,
'reg' if inference_method is None else inference_method, str(wins), Q, back_cstr, str(nDims))
if back_cstr == True:
model_file_name += '--MLP_dims=%s' % (MLP_dims,)
print('Model file name: ', model_file_name)
print(m)
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# Here layer numbers are different than in initialization. 0-th layer is the top one
for i in range(m.nLayers):
m.layers[i].kern.inv_l[:] = np.mean( 1./((m.layers[i].X.mean.values.max(0)-m.layers[i].X.mean.values.min(0))/np.sqrt(2.)) )
m.layers[i].likelihood.variance[:] = 0.01*out_train.var()
m.layers[i].kern.variance.fix(warning=False)
m.layers[i].likelihood.fix(warning=False)
print(m)
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print(m.layer_1.kern.inv_l)
print(m.layer_0.kern.inv_l)
print( np.mean(1./((m.layer_1.X.mean.values.max(0)-m.layer_1.X.mean.values.min(0))/np.sqrt(2.))) )
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# Plot initialization of hidden layer:
def plot_hidden_states(fig_no, layer, layer_start_point=None, layer_end_point=None,
data_start_point=None, data_end_point=None):
if layer_start_point is None: layer_start_point=0;
if layer_end_point is None: layer_end_point = len(layer.mean)
if data_start_point is None: data_start_point=0;
if data_end_point is None: layer_end_point = len(out_train)
data = out_train[data_start_point:data_end_point]
layer_means = layer.mean[layer_start_point:layer_end_point]
layer_vars = layer.variance[layer_start_point:layer_end_point]
fig4 = plt.figure(fig_no,figsize=(10,8))
ax1 = plt.subplot(1,1,1)
fig4.suptitle('Hidden layer plotting')
ax1.plot(out_train[data_start_point:data_end_point], label="Orig data Train_out", color = 'b')
ax1.plot( layer_means, label = 'pred mean', color = 'r' )
ax1.plot( layer_means +\
2*np.sqrt( layer_vars ), label = 'pred var', color='r', linestyle='--' )
ax1.plot( layer_means -\
2*np.sqrt( layer_vars ), label = 'pred var', color='r', linestyle='--' )
ax1.legend(loc=4)
ax1.set_title('Hidden layer vs Training data')
del ax1
plot_hidden_states(5,m.layer_1.qX_0)
#plot_hidden_states(6,m.layer_2.qX_0)
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#init_runs = 50 if out_train.shape[0]<1000 else 100
init_runs = 10
print("Init runs: ", init_runs)
m.optimize('bfgs',messages=1,max_iters=init_runs)
for i in range(m.nLayers):
m.layers[i].kern.variance.constrain_positive(warning=False)
m.layers[i].likelihood.constrain_positive(warning=False)
m.optimize('bfgs',messages=1,max_iters=10000)
print(m)
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print(m)
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if hasattr(m, 'layer_1'):
print("Layer 1: ")
print("States means (min and max), shapes: ", m.layer_1.qX_0.mean.min(),
m.layer_1.qX_0.mean.max(), m.layer_1.qX_0.mean.shape)
print("States variances (min and max), shapes: ", m.layer_1.qX_0.variance.min(),
m.layer_1.qX_0.variance.max(), m.layer_1.qX_0.mean.shape)
print("Inverse langthscales (min and max), shapes: ", m.layer_1.rbf.inv_lengthscale.min(),
m.layer_1.rbf.inv_lengthscale.max(), m.layer_1.rbf.inv_lengthscale.shape )
if hasattr(m, 'layer_0'):
print("")
print("Layer 0 (output): ")
print("Inverse langthscales (min and max), shapes: ", m.layer_0.rbf.inv_lengthscale.min(),
m.layer_0.rbf.inv_lengthscale.max(), m.layer_0.rbf.inv_lengthscale.shape )
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print(m.layer_0.rbf.inv_lengthscale)
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print(m.layer_1.rbf.inv_lengthscale)
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# Free-run on the train data
# initialize to last part of trained latent states
#init_Xs = [None, m.layer_1.qX_0[0:win_out]] # init_Xs for train prediction
# initialize to zeros
init_Xs = None
predictions_train = m.freerun(init_Xs = init_Xs, U=in_train, m_match=True)
# initialize to last part of trainig latent states
#init_Xs = [None, m.layer_1.qX_0[-win_out:] ] # init_Xs for test prediction
#U_test = np.vstack( (in_train[-win_in:], in_test) )
# initialize to zeros
init_Xs = None
U_test = in_test
# Free-run on the test data
predictions_test = m.freerun(init_Xs = init_Xs, U=U_test, m_match=True)
del init_Xs, U_test
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# Plot predictions
def plot_predictions(fig_no,posterior_train, posterior_test=None, layer_no = None):
"""
Plots the output data along with posterior of the layer.
Used for plotting the hidden states or
layer_no: int or Normal posterior
plot states of this layer (0-th is output). There is also some logic about compting
the MSE, and aligning with actual data.
"""
if layer_no is None: #default
layer_no = 1
if posterior_test is None:
no_test_data = True
else:
no_test_data = False
if isinstance(posterior_train, list):
layer_in_list = len(predictions_train)-1-layer_no # standard layer no (like in printing the model)
predictions_train_layer = predictions_train[layer_in_list]
else:
predictions_train_layer = posterior_train
if not no_test_data:
if isinstance(posterior_test, list):
predictions_test_layer = predictions_test[layer_in_list]
else:
predictions_test_layer = posterior_test
if layer_no == 0:
pred_ind_start=0; orig_data_ind_start=win_out
else:
pred_ind_start=0; orig_data_ind_start=0
if layer_no == 0:
# Compute RMSE ignoring first output values of length "win_out"
train_rmse = [comp_RMSE(predictions_train_layer.mean[pred_ind_start+win_out:],
out_train[orig_data_ind_start+win_out:])]
print("Train overall RMSE: ", str(train_rmse))
if not no_test_data:
# Compute RMSE ignoring first output values of length "win_out"
try:
test_rmse = [comp_RMSE(predictions_test_layer.mean[pred_ind_start+win_out:],
out_test[orig_data_ind_start+win_out:])]
except ValueError as ee: # length of predicted and test are equal. When we start from previous.
test_rmse = [comp_RMSE(predictions_test_layer.mean[pred_ind_start+win_out:],
out_test[-win_out + orig_data_ind_start+win_out:])]
print("Test overall RMSE: ", str(test_rmse))
# Plot predictions:
if not no_test_data:
fig5 = plt.figure(10,figsize=(20,8))
else:
fig5 = plt.figure(10,figsize=(10,8))
fig5.suptitle('Predictions on Training and Test data')
if not no_test_data:
ax1 = plt.subplot(1,2,1)
else:
ax1 = plt.subplot(1,1,1)
ax1.plot(out_train[orig_data_ind_start:], label="Train_out", color = 'b')
ax1.plot( predictions_train_layer.mean, label = 'pred mean', color = 'r' )
ax1.plot( predictions_train_layer.mean +\
2*np.sqrt( predictions_train_layer.variance ), label = 'pred var', color='r', linestyle='--' )
ax1.plot( predictions_train_layer.mean -\
2*np.sqrt( predictions_train_layer.variance ), label = 'pred var', color='r', linestyle='--' )
ax1.legend(loc=4)
ax1.set_title('Predictions on Train')
if not no_test_data:
ax2 = plt.subplot(1,2,2)
ax2.plot(out_test[orig_data_ind_start:], label="Test_out", color = 'b')
ax2.plot( predictions_test_layer.mean, label = 'pred mean', color = 'r' )
#ax2.plot( predictions_test_layer.mean +\
# 2*np.sqrt( predictions_test_layer.variance ), label = 'pred var', color='r', linestyle='--' )
#ax2.plot( predictions_test_layer.mean -\
# 2*np.sqrt( predictions_test_layer.variance ), label = 'pred var', color='r', linestyle='--' )
ax2.legend(loc=4)
ax2.set_title('Predictions on Test')
del ax2
del ax1
plot_predictions(7,predictions_train, predictions_test , layer_no = 0)
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In [31]:
plot_predictions(7,predictions_train, predictions_test , layer_no = 0)
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comp_RMSE(np.zeros( (len(out_train[20:]),1) ), out_train[20:] )
Out[32]:
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out_train[20:].mean(0)
Out[33]:
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plot_hidden_states(8,m.layer_1.qX_0)
#plot_hidden_states(9,m.layer_2.qX_0)
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