SelectKBest sklearn varying computation times - machine-learning

I was trying to do feature selection on a synthetic multilabel dataset. It was observed that the computation time for giving the complete dataset to SelectKBest was much higher as compared to time required while giving one feature at a time. In this example below only one label (or target variable) is considered.
import pandas as pd
from sklearn.datasets import make_multilabel_classification
from sklearn.feature_selection import chi2, SelectKBest, f_classif
# Generate a multilabel dataset
x, y = make_multilabel_classification(n_samples=40000, n_features = 1000, sparse = False, n_labels = 4, n_classes = 9,
return_indicator = 'dense', allow_unlabeled = True, random_state = 1000)
X_df = pd.DataFrame(x)
y_df = pd.DataFrame(y)
%%time
selected_features2 = []
for label in y_df.columns.tolist()[0:1]:
selector = SelectKBest(f_classif, k='all')
selected_features = []
for ftr in X_df.columns.tolist():
selector.fit(X_df[[ftr]], y_df[label])
selected_features.extend(np.round(selector.scores_,4))
CPU times: user 3.2 s, sys: 0 ns, total: 3.2 s . Wall time: 3.18 s
%%time
sel_features = []
for label in y_df.columns.tolist()[0:1]:
selector = SelectKBest(f_classif, k='all')
selector.fit(X_df, y_df[label])
sel_features.extend(np.round(selector.scores_,4))
CPU times: user 208 ms, sys: 37.2 s, total: 37.4 s Wall time: 37.4 s
%%time
sel_features = []
for label in y_df.columns.tolist()[0:1]:
selector = SelectKBest(f_classif, k='all')
selector.fit(X_df.as_matrix(), y_df[label].as_matrix())
sel_features.extend(np.round(selector.scores_,4))
CPU times: user 220 ms, sys: 35.4 s, total: 35.7 s Wall time: 35.6 s .
Why is there this much difference in the computation times?

Related

Sklearn Pipeline - eliminating the redundant reruns of some steps in GridSearchCV

Could anyone suggest an elegant way to eliminate the redundant reruns in a pipeline. The example below shows that MyLogistic.fit() is called 37 times (36 for the CV + 1 on the whole data set). For instance, if we take the hyperparameters:
(0.2, 1, 0.01)
(0.2, 1, 0.5)
then it's not necessary to rerun the first step, MyLogistic, with C = 0.2, because its result will be the same (let's ignore the random seed issue). The same reasoning applies to any combination of the first k hyperparameters: once we got the result from the first k steps, we can recycle it.
Thanks to Ben's suggestion, I used the "memory" argument in Pipeline and the count of calls got reduced to 12 (13). Apparently that's because there are 4 combinations of select_k* parameters, times 3 folds. But, for C = 0.02 there is no need to call MyLogistic() twice for max_features 1 and 2. Is there a more or less elegant way to avoid
those redundant calls also?
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import (GridSearchCV, StratifiedKFold)
from sklearn.feature_selection import SelectFromModel
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.datasets import load_iris
import numpy as np
class MyLogistic(LogisticRegression):
__call_counter = 0
def fit(self, X, y, sample_weight=None):
print("MyLogistic fit is called.")
MyLogistic._MyLogistic__call_counter += 1
# fit() returns self.
return super().fit(X, y, sample_weight)
# If I use this "extension", everything works fine.
#class MyLogistic(LogisticRegression):
# pass
initial_logistic = MyLogistic(solver="liblinear", random_state = np.random.RandomState(18))
final_logistic = LogisticRegression(solver="liblinear", random_state = np.random.RandomState(20))
# prefit = False by default
select_best = SelectFromModel(estimator = initial_logistic, threshold = -np.inf)
select_k_best_pipeline = Pipeline(steps=[
('first_scaler', StandardScaler(with_mean = False)),
# initial_logistic will be called from select_best, prefit = false by default.
('select_k_best', select_best),
('final_logit', final_logistic)
])
select_best_grid = {'select_k_best__estimator__C' : [0.02, 0.03],
'select_k_best__max_features': [1, 2],
'final_logit__C' : [0.01, 0.5, 1.0]}
skf = StratifiedKFold(n_splits = 3, shuffle = True, random_state = 17)
# Use n_jobs = 1 to get the correct count of calls
logit_best_searcher = GridSearchCV(estimator = select_k_best_pipeline, param_grid = select_best_grid, cv = skf,
scoring = "roc_auc", n_jobs = 1, verbose = 4)
X, y = load_iris(return_X_y=True)
logit_best_searcher.fit(X, y > 0)
print("Best hyperparams: ", logit_best_searcher.best_params_)
print("The count of calls is: ", MyLogistic._MyLogistic__call_counter)

Anomalies Detection by DBSCAN

I am using DBSCAN on my training datatset in order to find outliers and remove those outliers from the dataset before training model. I am using DBSCAN on my train rows 7697 with 8 columns.Here is my code
from sklearn.cluster import DBSCAN
X = StandardScaler().fit_transform(X_train[all_features])
model = DBSCAN(eps=0.3 , min_samples=10).fit(X)
print (model)
X_train_1=X_train.drop(X_train[model.labels_==-1].index).copy()
X_train_1.reset_index(drop=True,inplace=True)
Q-1 Out of these 7 some are discrete and some are continuous , is it ok to scale discrete and continuous both or just continuous?
Q-2 Do i need to map cluster to test data as it learned from training?
DBSCAN will handle those outliers for you. That's what is was built for. See the example below and post back if you have additional questions.
import seaborn as sns
import pandas as pd
titanic = sns.load_dataset('titanic')
titanic = titanic.copy()
titanic = titanic.dropna()
titanic['age'].plot.hist(
bins = 50,
title = "Histogram of the age variable"
)
from scipy.stats import zscore
titanic["age_zscore"] = zscore(titanic["age"])
titanic["is_outlier"] = titanic["age_zscore"].apply(
lambda x: x <= -2.5 or x >= 2.5
)
titanic[titanic["is_outlier"]]
ageAndFare = titanic[["age", "fare"]]
ageAndFare.plot.scatter(x = "age", y = "fare")
from sklearn.preprocessing import MinMaxScaler
scaler = MinMaxScaler()
ageAndFare = scaler.fit_transform(ageAndFare)
ageAndFare = pd.DataFrame(ageAndFare, columns = ["age", "fare"])
ageAndFare.plot.scatter(x = "age", y = "fare")
from sklearn.cluster import DBSCAN
outlier_detection = DBSCAN(
eps = 0.5,
metric="euclidean",
min_samples = 3,
n_jobs = -1)
clusters = outlier_detection.fit_predict(ageAndFare)
clusters
from matplotlib import cm
cmap = cm.get_cmap('Accent')
ageAndFare.plot.scatter(
x = "age",
y = "fare",
c = clusters,
cmap = cmap,
colorbar = False
)

Batch Training Accuracy is always multiple of 10%

So I am training a CNN and compute the training accuracy for each batch. Most of the it gives out 100% batch training accuracy. which I though was okay because I'm testing my model against the data I trained it with. But at some iterations, I get a 90% or 90% batch training accuracy. And worst, sometimes it goes down to 0% real quick and bounces back to 100% batch training accuracy. And I used the algorithm in https://github.com/Hvass-Labs/TensorFlow-Tutorials/blob/master/04_Save_Restore.ipynb and they also computed the batch training accuracy but they don't get the same results I get. They started out with around 80% batch training accuracy and observed a gradual increase until 98%. Why is this?
I was suspecting that my network is overfitting.
Here is my exact code:
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from scipy import stats
import tensorflow as tf
import pyfftw
from scipy import signal
import xlrd
from tensorflow.python.tools import freeze_graph
from tensorflow.python.tools import optimize_for_inference_lib
import time
from datetime import timedelta
import math
import os
from sklearn.metrics import confusion_matrix
##matplotlib inline
plt.style.use('ggplot')
## define funtions
def read_data(file_path):
## column_names = ['user-id','activity','timestamp', 'x-axis', 'y-axis', 'z-axis']
column_names = ['activity','timestamp', 'Ax', 'Ay', 'Az', 'Gx', 'Gy', 'Gz', 'Mx', 'My', 'Mz'] ## 3 sensors
data = pd.read_csv(file_path,header = None, names = column_names)
return data
def feature_normalize(dataset):
mu = np.mean(dataset,axis = 0)
sigma = np.std(dataset,axis = 0)
return (dataset - mu)/sigma
def plot_axis(ax, x, y, title):
ax.plot(x, y)
ax.set_title(title)
ax.xaxis.set_visible(False)
ax.set_ylim([min(y) - np.std(y), max(y) + np.std(y)])
ax.set_xlim([min(x), max(x)])
ax.grid(True)
def plot_activity(activity,data):
fig, (ax0, ax1, ax2) = plt.subplots(nrows = 3, figsize = (15, 10), sharex = True)
plot_axis(ax0, data['timestamp'], data['Ax'], 'x-axis')
plot_axis(ax1, data['timestamp'], data['Ay'], 'y-axis')
plot_axis(ax2, data['timestamp'], data['Az'], 'z-axis')
plt.subplots_adjust(hspace=0.2)
fig.suptitle(activity)
plt.subplots_adjust(top=0.90)
plt.show()
def windows(data, size):
start = 0
while start < data.count():
yield start, start + size
start += (size / 2)
def segment_signal(data, window_size = None, num_channels=None): # edited
segments = np.empty((0,window_size,num_channels)) #change from 3 to 9 channels for AGM fusion #use variable num_channels=9
labels = np.empty((0))
for (n_start, n_end) in windows(data['timestamp'], window_size):
## x = data["x-axis"][start:end]
## y = data["y-axis"][start:end]
## z = data["z-axis"][start:end]
n_start = int(n_start)
n_end = int(n_end)
Ax = data["Ax"][n_start:n_end]
Ay = data["Ay"][n_start:n_end]
Az = data["Az"][n_start:n_end]
Gx = data["Gx"][n_start:n_end]
Gy = data["Gy"][n_start:n_end]
Gz = data["Gz"][n_start:n_end]
Mx = data["Mx"][n_start:n_end]
My = data["My"][n_start:n_end]
Mz = data["Mz"][n_start:n_end]
if(len(dataset['timestamp'][n_start:n_end]) == window_size): # include only windows with size of 90
segments = np.vstack([segments,np.dstack([Ax,Ay,Az,Gx,Gy,Gz,Mx,My,Mz])])
labels = np.append(labels,stats.mode(data["activity"][n_start:n_end])[0][0])
return segments, labels
def weight_variable(shape):
initial = tf.truncated_normal(shape, stddev = 0.1)
return tf.Variable(initial)
def bias_variable(shape):
initial = tf.constant(0.0, shape = shape)
return tf.Variable(initial)
def depthwise_conv2d(x, W):
return tf.nn.depthwise_conv2d(x,W, [1, 1, 1, 1], padding='VALID')
def apply_depthwise_conv(x,weights,biases):
return tf.nn.relu(tf.add(depthwise_conv2d(x, weights),biases))
def apply_max_pool(x,kernel_size,stride_size):
return tf.nn.max_pool(x, ksize=[1, 1, kernel_size, 1],
strides=[1, 1, stride_size, 1], padding='VALID')
#------------------------get dataset----------------------#
## run shoaib_dataset.py to generate dataset_shoaib_total.txt
## get data from dataset_shoaib_total.txt
dataset = read_data('dataset_shoaib_total.txt')
#--------------------preprocessing------------------------#
dataset['Ax'] = feature_normalize(dataset['Ax'])
dataset['Ay'] = feature_normalize(dataset['Ay'])
dataset['Az'] = feature_normalize(dataset['Az'])
dataset['Gx'] = feature_normalize(dataset['Gx'])
dataset['Gy'] = feature_normalize(dataset['Gy'])
dataset['Gz'] = feature_normalize(dataset['Gz'])
dataset['Mx'] = feature_normalize(dataset['Mx'])
dataset['My'] = feature_normalize(dataset['My'])
dataset['Mz'] = feature_normalize(dataset['Mz'])
###--------------------plot activity data----------------#
##for activity in np.unique(dataset["activity"]):
## subset = dataset[dataset["activity"] == activity][:180]
## plot_activity(activity,subset)
#------------------fixed hyperparameters--------------------#
window_size = 200 #from 90 #FIXED at 4 seconds
#----------------input hyperparameters------------------#
input_height = 1
input_width = window_size
num_labels = 6
num_channels = 9 #from 3 channels #9 channels for AGM
#-------------------sliding time window----------------#
segments, labels = segment_signal(dataset, window_size=window_size, num_channels=num_channels)
labels = np.asarray(pd.get_dummies(labels), dtype = np.int8)
reshaped_segments = segments.reshape(len(segments), (window_size*num_channels)) #use variable num_channels instead of constant 3 channels
#------------divide data into test and training set-----------#
train_test_split = np.random.rand(len(reshaped_segments)) < 0.80
train_x_init = reshaped_segments[train_test_split]
train_y_init = labels[train_test_split]
test_x = reshaped_segments[~train_test_split]
test_y = labels[~train_test_split]
train_validation_split = np.random.rand(len(train_x_init)) < 0.80
train_x = train_x_init[train_validation_split]
train_y = train_y_init[train_validation_split]
validation_x = train_x_init[~train_validation_split]
validation_y = train_y_init[~train_validation_split]
#---------------training hyperparameters----------------#
batch_size = 10
kernel_size = 60 #from 60 #optimal 2
depth = 15 #from 60 #optimal 15
num_hidden = 1000 #from 1000 #optimal 80
learning_rate = 0.0001
training_epochs = 8
total_batches = train_x.shape[0] ##// batch_size
#---------define placeholders for input----------#
X = tf.placeholder(tf.float32, shape=[None,input_width * num_channels], name="input")
X_reshaped = tf.reshape(X,[-1,input_height,input_width,num_channels])
Y = tf.placeholder(tf.float32, shape=[None,num_labels])
#---------------------perform convolution-----------------#
# first convolutional layer
c_weights = weight_variable([1, kernel_size, num_channels, depth])
c_biases = bias_variable([depth * num_channels])
c = apply_depthwise_conv(X_reshaped,c_weights,c_biases)
p = apply_max_pool(c,20,2)
# second convolutional layer
c2_weights = weight_variable([1, 6,depth*num_channels,depth//10])
c2_biases = bias_variable([(depth*num_channels)*(depth//10)])
c = apply_depthwise_conv(p,c2_weights,c2_biases)
#--------------flatten data for fully connected layers----------#
shape = c.get_shape().as_list()
c_flat = tf.reshape(c, [-1, shape[1] * shape[2] * shape[3]])
#------------fully connected layers----------------#
f_weights_l1 = weight_variable([shape[1] * shape[2] * depth * num_channels * (depth//10), num_hidden])
f_biases_l1 = bias_variable([num_hidden])
f = tf.nn.tanh(tf.add(tf.matmul(c_flat, f_weights_l1),f_biases_l1))
#----------------------dropout------------------#
keep_prob = tf.placeholder(tf.float32)
drop_layer = tf.nn.dropout(f, keep_prob)
#----------------------softmax layer----------------#
out_weights = weight_variable([num_hidden, num_labels])
out_biases = bias_variable([num_labels])
y_ = tf.nn.softmax(tf.add(tf.matmul(drop_layer, out_weights),out_biases), name="y_")
#-----------------loss optimization-------------#
loss = -tf.reduce_sum(Y * tf.log(y_))
optimizer = tf.train.AdamOptimizer(learning_rate = learning_rate).minimize(loss)
#-----------------compute accuracy---------------#
correct_prediction = tf.equal(tf.argmax(y_,1), tf.argmax(Y,1))
accuracy = tf.reduce_mean(tf.cast(correct_prediction, tf.float32))
cost_history = np.empty(shape=[1],dtype=float)
saver = tf.train.Saver()
session = tf.Session()
session.run(tf.global_variables_initializer())
#-------------early stopping-----------------#
# Best validation accuracy seen so far.
best_validation_accuracy = 0.0
# Iteration-number for last improvement to validation accuracy.
last_improvement = 0
# Stop optimization if no improvement found in this many iterations.
require_improvement = 1000
# Counter for total number of iterations performed so far.
total_iterations = 0
def validation_accuracy():
return session.run(accuracy, feed_dict={X: validation_x, Y: validation_y, keep_prob: 1.0})
def next_batch(b, batch_size, train_x, train_y):
##for b in range(total_batches):
offset = (b * batch_size) % (train_y.shape[0] - batch_size)
batch_x = train_x[offset:(offset + batch_size), :]
batch_y = train_y[offset:(offset + batch_size), :]
return batch_x, batch_y
def optimize(num_iterations):
# Ensure we update the global variables rather than local copies.
global total_iterations
global best_validation_accuracy
global last_improvement
# Start-time used for printing time-usage below.
start_time = time.time()
for i in range(num_iterations):
# Increase the total number of iterations performed.
# It is easier to update it in each iteration because
# we need this number several times in the following.
total_iterations += 1
# Get a batch of training examples.
# x_batch now holds a batch of images and
# y_true_batch are the true labels for those images.
##x_batch, y_true_batch = data.train.next_batch(train_batch_size)
x_batch, y_true_batch = next_batch(i, batch_size, train_x, train_y)
# Put the batch into a dict with the proper names
# for placeholder variables in the TensorFlow graph.
feed_dict_train = {X: x_batch,
Y: y_true_batch, keep_prob: 0.5}
# Run the optimizer using this batch of training data.
# TensorFlow assigns the variables in feed_dict_train
# to the placeholder variables and then runs the optimizer.
session.run(optimizer, feed_dict=feed_dict_train)
# Print status every 100 iterations and after last iteration.
if (total_iterations % 100 == 0) or (i == (num_iterations - 1)):
# Calculate the accuracy on the training-batch.
acc_train = session.run(accuracy, feed_dict={X: x_batch,
Y: y_true_batch, keep_prob: 1.0})
# Calculate the accuracy on the validation-set.
# The function returns 2 values but we only need the first.
##acc_validation, _ = validation_accuracy()
acc_validation = validation_accuracy()
# If validation accuracy is an improvement over best-known.
if acc_validation > best_validation_accuracy:
# Update the best-known validation accuracy.
best_validation_accuracy = acc_validation
# Set the iteration for the last improvement to current.
last_improvement = total_iterations
# Save all variables of the TensorFlow graph to file.
saver.save(sess=session, save_path="../shoaib-har_agm_es.ckpt")
# A string to be printed below, shows improvement found.
improved_str = '*'
else:
# An empty string to be printed below.
# Shows that no improvement was found.
improved_str = ''
# Status-message for printing.
msg = "Iter: {0:>6}, Train-Batch Accuracy: {1:>6.1%}, Validation Acc: {2:>6.1%} {3}"
# Print it.
print(msg.format(i + 1, acc_train, acc_validation, improved_str))
# If no improvement found in the required number of iterations.
if total_iterations - last_improvement > require_improvement:
print("No improvement found in a while, stopping optimization.")
# Break out from the for-loop.
break
# Ending time.
end_time = time.time()
# Difference between start and end-times.
time_dif = end_time - start_time
# Print the time-usage.
print("Time usage: " + str(timedelta(seconds=int(round(time_dif)))))
optimize(10000)
With the output:
What exactly is training accuracy? Is it even computed? Or do you compute the training accuracy on the entire training data and not just the batch you trained your network with?
Here I printed the results such that it prints out the batch training accuracy and the training accuracy on the entire dataset set for every multiples of 20 iterations.
The data is divided to 3 sets: train, validation and test.
Batch training accuracy is computed on the train set (the difference between the label and the prediction).
Validation accuracy is the accuracy on the validation set.
The batch accuracy can be computed just after a forward pass in the network. The number of samples in one forward pass is the batch size. It is just a way to train models faster (mini-batch gradient descent)
Overfitting is when the model works really good on known data (training set) but performs poorly on new data.
As to the 10% multiples, it is just the printing format you are using.

value prediction with tensorflow and python

I have a data set which contains a list of stock prices. I need to use the tensorflow and python to predict the close price.
Q1: I have the following code which takes the first 2000 records as training and 2001 to 20000 records as test but I don't know how to change the code to do the prediction of the close price of today and 1 day later??? Please advise!
#!/usr/bin/env python2
import numpy as np
import pandas as pd
import tensorflow as tf
import matplotlib.pyplot as plt
def feature_scaling(input_pd, scaling_meathod):
if scaling_meathod == 'z-score':
scaled_pd = (input_pd - input_pd.mean()) / input_pd.std()
elif scaling_meathod == 'min-max':
scaled_pd = (input_pd - input_pd.min()) / (input_pd.max() -
input_pd.min())
return scaled_pd
def input_reshape(input_pd, start, end, batch_size, batch_shift, n_features):
temp_pd = input_pd[start-1: end+batch_size-1]
output_pd = map(lambda y : temp_pd[y:y+batch_size], xrange(0, end-start+1, batch_shift))
output_temp = map(lambda x : np.array(output_pd[x]).reshape([-1]), xrange(len(output_pd)))
output = np.reshape(output_temp, [-1, batch_size, n_features])
return output
def target_reshape(input_pd, start, end, batch_size, batch_shift, n_step_ahead, m_steps_pred):
temp_pd = input_pd[start+batch_size+n_step_ahead-2: end+batch_size+n_step_ahead+m_steps_pred-2]
print temp_pd
output_pd = map(lambda y : temp_pd[y:y+m_steps_pred], xrange(0, end-start+1, batch_shift))
output_temp = map(lambda x : np.array(output_pd[x]).reshape([-1]), xrange(len(output_pd)))
output = np.reshape(output_temp, [-1,1])
return output
def lstm(input, n_inputs, n_steps, n_of_layers, scope_name):
num_layers = n_of_layers
input = tf.transpose(input,[1, 0, 2])
input = tf.reshape(input,[-1, n_inputs])
input = tf.split(0, n_steps, input)
with tf.variable_scope(scope_name):
cell = tf.nn.rnn_cell.BasicLSTMCell(num_units=n_inputs)
cell = tf.nn.rnn_cell.MultiRNNCell([cell]*num_layers)
output, state = tf.nn.rnn(cell, input, dtype=tf.float32) yi1
output = output[-1]
return output
feature_to_input = ['open price', 'highest price', 'lowest price', 'close price','turnover', 'volume','mean price']
feature_to_predict = ['close price']
feature_to_scale = ['volume']
sacling_meathod = 'min-max'
train_start = 1
train_end = 1000
test_start = 1001
test_end = 20000
batch_size = 100
batch_shift = 1
n_step_ahead = 1
m_steps_pred = 1
n_features = len(feature_to_input)
lstm_scope_name = 'lstm_prediction'
n_lstm_layers = 1
n_pred_class = 1
learning_rate = 0.1
EPOCHS = 1000
PRINT_STEP = 100
read_data_pd = pd.read_csv('./stock_price.csv')
temp_pd = feature_scaling(input_pd[feature_to_scale],sacling_meathod)
input_pd[feature_to_scale] = temp_pd
train_input_temp_pd = input_pd[feature_to_input]
train_input_nparr = input_reshape(train_input_temp_pd,
train_start, train_end, batch_size, batch_shift, n_features)
train_target_temp_pd = input_pd[feature_to_predict]
train_target_nparr = target_reshape(train_target_temp_pd, train_start, train_end, batch_size, batch_shift, n_step_ahead, m_steps_pred)
test_input_temp_pd = input_pd[feature_to_input]
test_input_nparr = input_reshape(test_input_temp_pd, test_start, test_end, batch_size, batch_shift, n_features)
test_target_temp_pd = input_pd[feature_to_predict]
test_target_nparr = target_reshape(test_target_temp_pd, test_start, test_end, batch_size, batch_shift, n_step_ahead, m_steps_pred)
tf.reset_default_graph()
x_ = tf.placeholder(tf.float32, [None, batch_size, n_features])
y_ = tf.placeholder(tf.float32, [None, 1])
lstm_output = lstm(x_, n_features, batch_size, n_lstm_layers, lstm_scope_name)
W = tf.Variable(tf.random_normal([n_features, n_pred_class]))
b = tf.Variable(tf.random_normal([n_pred_class]))
y = tf.matmul(lstm_output, W) + b
cost_func = tf.reduce_mean(tf.square(y - y_))
train_op = tf.train.GradientDescentOptimizer(learning_rate).minimize(cost_func)
optimizer = tf.train.GradientDescentOptimizer(learning_rate).minimize(loss, global_step=global_step)
init = tf.initialize_all_variables()
with tf.Session() as sess:
sess.run(init)
for ii in range(EPOCHS):
sess.run(train_op, feed_dict={x_:train_input_nparr, y_:train_target_nparr})
if ii % PRINT_STEP == 0:
cost = sess.run(cost_func, feed_dict={x_:train_input_nparr, y_:train_target_nparr})
print 'iteration =', ii, 'training cost:', cost
Very simply, prediction (a.k.a. scoring or inference) comes from running the input through only the forward pass, and collecting the score for each input vector. It's the same process flow as testing. The difference is the four stages of model use:
Train: learn from the training data set; adjust weights as needed.
Test: evaluate the model's performance; if accuracy has converged, stop training.
Validate: evaluate the accuracy of the trained model. If it doesn't meet acceptance criteria, change something and start over with the training.
Predict: you've passed validation -- release the model for use by the intended application.
All four steps follow the same forward logic flow; training includes back-propagation; the others do not. Simply follow the forward-only process, and you'll get the result form you need.
I worry about your data partition: only 10% for training, 90% for testing, and none for validation. A more typical split is 50-30-20, or something in that general area.
Q-1 : You should change your LSTM parameter to return a sequence of size two which will be prediction for that day and the day after.
Q-2 it's clearly that your model is underfitting the data, which is so obvious with your 10% train 90% test data ! You should more equilibrated ratio as suggested in the previous answer.

Keras LSTM RNN forecast - Shifting fitted forecast backward

I am trying to use LSTM Recurrent Neural Net using Keras to forecast future purchase. My input variables are time-window of purchases for previous 5 days, and a categorical variable which I encoded as dummy variables A, B, ...,I. My input data looks like following:
>>> dataframe.head()
day price A B C D E F G H I TS_bigHolidays
0 2015-06-16 7.031160 1 0 0 0 0 0 0 0 0 0
1 2015-06-17 10.732429 1 0 0 0 0 0 0 0 0 0
2 2015-06-18 21.312692 1 0 0 0 0 0 0 0 0 0
My problem is my forecasts/fitted values (both for trained and test data) seem to be shifted forward. Here is a plot:
My question is what parameter in LSTM Keras should I change to correct this issue? Or do I need to change anything in my input data?
Here is my code:
import numpy as np
import os
import matplotlib.pyplot as plt
import pandas
import math
import time
import csv
from keras.models import Sequential
from keras.layers.core import Dense, Activation, Dropout
from keras.layers.recurrent import LSTM
from sklearn.preprocessing import MinMaxScaler
np.random.seed(1234)
exo_feature = ["A","B","C","D","E","F","G","H","I", "TS_bigHolidays"]
look_back = 5 #this is number of days we are looking back for sliding window of time series
forecast_period_length = 40
# load the dataset
dataframe = pandas.read_csv('processedDataframeGameSphere.csv', header = 0, engine='python', skipfooter=6)
dataframe["price"] = dataframe['price'].astype('float32')
scaler = MinMaxScaler(feature_range=(0, 100))
dataframe["price"] = scaler.fit_transform(dataframe['price'])
# this function is used to make sliding window for time series data
def create_dataframe(dataframe, look_back=1):
dataX, dataY = [], []
for i in range(dataframe.shape[0]-look_back-1):
price_lookback = dataframe['price'][i: (i + look_back)] #i+look_back is exclusive here
exog_feature = dataframe[exo_feature].ix[i + look_back - 1] #Y is i+ look_back ,that's why
row_i = price_lookback.append(exog_feature)
dataX.append(row_i)
dataY.append(dataframe["price"][i + look_back])
return np.array(dataX), np.array(dataY)
window_dataframe, Y = create_dataframe(dataframe, look_back)
# split into train and test sets
train_size = int(dataframe.shape[0] - forecast_period_length) #28 is the number of days we want to forecast , 4 weeks
test_size = dataframe.shape[0] - train_size
test_size_start_point_with_lookback = train_size - look_back
trainX, trainY = window_dataframe[0:train_size,:], Y[0:train_size]
print(trainX.shape)
print(trainY.shape)
#below changed datawindowY indexing, since it's just array.
testX, testY = window_dataframe[train_size:dataframe.shape[0],:], Y[train_size:dataframe.shape[0]]
# reshape input to be [samples, time steps, features]
trainX = np.reshape(trainX, (trainX.shape[0], 1, trainX.shape[1]))
testX = np.reshape(testX, (testX.shape[0], 1, testX.shape[1]))
print(trainX.shape)
print(testX.shape)
# create and fit the LSTM network
dimension_input = testX.shape[2]
model = Sequential()
layers = [dimension_input, 50, 100, 1]
epochs = 100
model.add(LSTM(
input_dim=layers[0],
output_dim=layers[1],
return_sequences=True))
model.add(Dropout(0.2))
model.add(LSTM(
layers[2],
return_sequences=False))
model.add(Dropout(0.2))
model.add(Dense(
output_dim=layers[3]))
model.add(Activation("linear"))
start = time.time()
model.compile(loss="mse", optimizer="rmsprop")
print "Compilation Time : ", time.time() - start
model.fit(
trainX, trainY,
batch_size= 10, nb_epoch=epochs, validation_split=0.05,verbose =2)
# Estimate model performance
trainScore = model.evaluate(trainX, trainY, verbose=0)
trainScore = math.sqrt(trainScore)
trainScore = scaler.inverse_transform(np.array([[trainScore]]))
print('Train Score: %.2f RMSE' % (trainScore))
testScore = model.evaluate(testX, testY, verbose=0)
testScore = math.sqrt(testScore)
testScore = scaler.inverse_transform(np.array([[testScore]]))
print('Test Score: %.2f RMSE' % (testScore))
# generate predictions for training
trainPredict = model.predict(trainX)
testPredict = model.predict(testX)
# shift train predictions for plotting
np_price = np.array(dataframe["price"])
print(np_price.shape)
np_price = np_price.reshape(np_price.shape[0],1)
trainPredictPlot = np.empty_like(np_price)
trainPredictPlot[:, :] = np.nan
trainPredictPlot[look_back:len(trainPredict)+look_back, :] = trainPredict
testPredictPlot = np.empty_like(np_price)
testPredictPlot[:, :] = np.nan
testPredictPlot[len(trainPredict)+look_back+1:dataframe.shape[0], :] = testPredict
# plot baseline and predictions
plt.plot(dataframe["price"])
plt.plot(trainPredictPlot)
plt.plot(testPredictPlot)
plt.show()
It's not a problem of LSTM, if you use just simple feed-forward network, the effect will be the same.
the problem is the network tend to mimic yesterday value instead of 'forecasting' you expect.
(it is nice strategy in term of reducing MSE loss)
you need more 'care' to avoid this issue and it's not a simple issue.

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