Cleaned up imports

Author: eriklindernoren

README.md

@@ -252,7 +252,7 @@ but rather to present the inner workings of them in a transparent way.
 - [Deep Q-Network](mlfromscratch/reinforcement_learning/deep_q_network.py)
 
 ### Deep Learning
-  + [Base Class](mlfromscratch/deep_learning/neural_network.py)
+  + [Neural Network](mlfromscratch/deep_learning/neural_network.py)
   + [Layers](mlfromscratch/deep_learning/layers.py)
     * Activation Layer
     * Average Pooling Layer

mlfromscratch/deep_learning/activation_functions.py

@@ -1,5 +1,4 @@
 import numpy as np
-import sys
 
 # Collection of activation functions
 # Reference: https://en.wikipedia.org/wiki/Activation_function
@@ -31,7 +30,6 @@ def function(self, x):
         return 2 / (1 + np.exp(-2*x)) - 1
 
     def gradient(self, x):
-        # Avoid overflow for large inputs
         return 1 - np.power(self.function(x), 2)
 
 class ReLU():
@@ -64,8 +62,8 @@ def gradient(self, x):
         return np.where(x >= 0.0, 1, self.function(x) + self.alpha)
 
 class SELU():
-    # Reference :   https://arxiv.org/abs/1706.02515,
-    #               https://github.com/bioinf-jku/SNNs/blob/master/SelfNormalizingNetworks_MLP_MNIST.ipynb
+    # Reference : https://arxiv.org/abs/1706.02515,
+    # https://github.com/bioinf-jku/SNNs/blob/master/SelfNormalizingNetworks_MLP_MNIST.ipynb
     def __init__(self):
         self.alpha = 1.6732632423543772848170429916717
         self.scale = 1.0507009873554804934193349852946 
@@ -83,5 +81,5 @@ def function(self, x):
         return np.log(1 + np.exp(x))
 
     def gradient(self, x):
-        return Sigmoid().function(x)
+        return 1 / (1 + np.exp(-x))
 

mlfromscratch/deep_learning/layers.py

@@ -1,11 +1,10 @@
 
 from __future__ import print_function, division
-import sys
-import os
 import math
 import numpy as np
 import copy
-from mlfromscratch.deep_learning.activation_functions import Sigmoid, ReLU, SoftPlus, LeakyReLU, TanH, ELU, SELU, Softmax
+from mlfromscratch.deep_learning.activation_functions import Sigmoid, ReLU, SoftPlus, LeakyReLU
+from mlfromscratch.deep_learning.activation_functions import TanH, ELU, SELU, Softmax
 
 
 class Layer(object):

mlfromscratch/deep_learning/loss_functions.py

@@ -1,6 +1,6 @@
 from __future__ import division
 import numpy as np
-from mlfromscratch.utils.data_operation import accuracy_score
+from mlfromscratch.utils import accuracy_score
 from mlfromscratch.deep_learning.activation_functions import Sigmoid
 
 class Loss(object):

mlfromscratch/deep_learning/neural_network.py

@@ -1,13 +1,8 @@
 from __future__ import print_function
 from terminaltables import AsciiTable
-import copy
 import numpy as np
 import progressbar
-
-# Import helper functions
-from mlfromscratch.utils.data_manipulation import train_test_split, to_categorical, normalize
-from mlfromscratch.utils.data_manipulation import get_random_subsets, shuffle_data, batch_iterator
-from mlfromscratch.utils.data_operation import accuracy_score
+from mlfromscratch.utils import batch_iterator
 from mlfromscratch.deep_learning.loss_functions import CrossEntropy
 from mlfromscratch.utils.misc import bar_widgets
 
@@ -30,7 +25,7 @@ def __init__(self, optimizer, loss=CrossEntropy, validation_data=None):
         self.layers = []
         self.errors = {"training": [], "validation": []}
         self.loss_function = loss()
-        
+
         self.validation_set = False
         if validation_data:
             self.validation_set = True
@@ -47,50 +42,41 @@ def add(self, layer):
         # to the output shape of the last added layer
         if self.layers:
             layer.set_input_shape(shape=self.layers[-1].output_shape())
-
         # If the layer has weights that needs to be initialized 
         if hasattr(layer, 'initialize'):
             layer.initialize(optimizer=self.optimizer)
-
         # Add layer to the network
         self.layers.append(layer)
 
     def train_on_batch(self, X, y):
-        # Calculate output
         y_pred = self._forward_pass(X)
-        # Calculate the training loss
+        # Calculate the loss and accuracy of the prediction
         loss = np.mean(self.loss_function.loss(y, y_pred))
+        acc = self.loss_function.acc(y, y_pred)
         # Calculate the gradient of the loss function wrt y_pred
         loss_grad = self.loss_function.gradient(y, y_pred)
-        # Calculate the accuracy of the prediction
-        acc = self.loss_function.acc(y, y_pred)
-        # Backprop. Update weights
+        # Backpropagate. Update weights
         self._backward_pass(loss_grad=loss_grad)
 
         return loss, acc
 
-
     def fit(self, X, y, n_epochs, batch_size):
-
         n_samples = np.shape(X)[0]
         n_batches = int(n_samples / batch_size)
 
         bar = progressbar.ProgressBar(widgets=bar_widgets)
         for _ in bar(range(n_epochs)):
-            idx = range(n_samples)
-            np.random.shuffle(idx)
-
-            batch_t_error = 0   # Mean batch training error
+            batch_error = 0
             for X_batch, y_batch in batch_iterator(X, y, batch_size=batch_size):
                 loss, _ = self.train_on_batch(X_batch, y_batch)
-                batch_t_error += loss
+                batch_error += loss
+
+            self.errors["training"].append(batch_error / n_batches)
 
-            # Save the epoch mean error
-            self.errors["training"].append(batch_t_error / n_batches)
             if self.validation_set:
                 # Determine validation error
-                y_val_p = self._forward_pass(self.X_val)
-                validation_loss = np.mean(self.loss_function.loss(self.y_val, y_val_p))
+                y_val_pred = self._forward_pass(self.X_val)
+                validation_loss = np.mean(self.loss_function.loss(self.y_val, y_val_pred))
                 self.errors["validation"].append(validation_loss)
 
         return self.errors["training"], self.errors["validation"]
@@ -116,7 +102,7 @@ def summary(self, name="Model Summary"):
         print (AsciiTable([[name]]).table)
         # Network input shape (first layer's input shape)
         print ("Input Shape: %s" % str(self.layers[0].input_shape))
-        # Get each layer's configuration
+        # Iterate through network and get each layer's configuration
         table_data = [["Layer Type", "Parameters", "Output Shape"]]
         tot_params = 0
         for layer in self.layers:
@@ -125,10 +111,8 @@ def summary(self, name="Model Summary"):
             out_shape = layer.output_shape()
             table_data.append([layer_name, str(params), str(out_shape)])
             tot_params += params
-
         # Print network configuration table
         print (AsciiTable(table_data).table)
-
         print ("Total Parameters: %d\n" % tot_params)
 
     def predict(self, X):

mlfromscratch/deep_learning/optimizers.py

@@ -1,5 +1,5 @@
 import numpy as np
-from mlfromscratch.utils.data_manipulation import make_diagonal, normalize
+from mlfromscratch.utils import make_diagonal, normalize
 
 # Optimizers for models that use gradient based methods for finding the 
 # weights that minimizes the loss.

mlfromscratch/examples/convolutional_neural_network.py

@@ -7,13 +7,12 @@
 
 # Import helper functions
 from mlfromscratch.deep_learning import NeuralNetwork
-from mlfromscratch.utils.data_manipulation import train_test_split, to_categorical, normalize
-from mlfromscratch.utils.data_manipulation import get_random_subsets, shuffle_data
+from mlfromscratch.utils import train_test_split, to_categorical, normalize
+from mlfromscratch.utils import get_random_subsets, shuffle_data, Plot
 from mlfromscratch.utils.data_operation import accuracy_score
 from mlfromscratch.deep_learning.optimizers import StochasticGradientDescent, Adam, RMSprop, Adagrad, Adadelta
 from mlfromscratch.deep_learning.loss_functions import CrossEntropy
 from mlfromscratch.utils.misc import bar_widgets
-from mlfromscratch.utils import Plot
 from mlfromscratch.deep_learning.layers import Dense, Dropout, Conv2D, Flatten, Activation, MaxPooling2D
 from mlfromscratch.deep_learning.layers import AveragePooling2D, ZeroPadding2D, BatchNormalization, RNN
 
@@ -25,7 +24,7 @@ def main():
     # Conv Net
     #----------
 
-    optimizer = Adadelta()
+    optimizer = Adam()
 
     data = datasets.load_digits()
     X = data.data
@@ -62,7 +61,6 @@ def main():
     clf.add(BatchNormalization())
     clf.add(Dense(10))
     clf.add(Activation('softmax'))
-
     print ()
     clf.summary(name="ConvNet")
 

mlfromscratch/examples/decision_tree_classifier.py

@@ -6,10 +6,8 @@
 import os
 
 # Import helper functions
-from mlfromscratch.utils.data_manipulation import train_test_split, standardize
-from mlfromscratch.utils.data_operation import accuracy_score
-from mlfromscratch.utils.data_operation import mean_squared_error, calculate_variance
-from mlfromscratch.utils import Plot
+from mlfromscratch.utils import train_test_split, standardize, accuracy_score
+from mlfromscratch.utils import mean_squared_error, calculate_variance, Plot
 from mlfromscratch.supervised_learning import ClassificationTree
 
 def main():

mlfromscratch/examples/decision_tree_regressor.py

@@ -1,16 +1,10 @@
 from __future__ import division, print_function
 import numpy as np
-from sklearn import datasets
 import matplotlib.pyplot as plt
 import pandas as pd
-import sys
-import os
-
-# Import helper functions
-from mlfromscratch.utils.data_manipulation import train_test_split, standardize
-from mlfromscratch.utils.data_operation import accuracy_score
-from mlfromscratch.utils.data_operation import mean_squared_error, calculate_variance
-from mlfromscratch.utils import Plot
+
+from mlfromscratch.utils import train_test_split, standardize, accuracy_score
+from mlfromscratch.utils import mean_squared_error, calculate_variance, Plot
 from mlfromscratch.supervised_learning import RegressionTree
 
 def main():

mlfromscratch/examples/deep_q_network.py

@@ -1,14 +1,6 @@
 from __future__ import print_function
-import sys
-import os
-import math
-import random
 import numpy as np
-import progressbar
-import gym
-from collections import deque
-
-from mlfromscratch.utils.data_manipulation import to_categorical
+from mlfromscratch.utils import to_categorical
 from mlfromscratch.deep_learning.optimizers import Adam
 from mlfromscratch.deep_learning.loss_functions import SquareLoss
 from mlfromscratch.deep_learning.layers import Dense, Dropout, Flatten, Activation, Reshape, BatchNormalization

mlfromscratch/examples/demo.py

@@ -1,13 +1,11 @@
 from __future__ import print_function
-import sys, os
 from sklearn import datasets
 import numpy as np
-import pandas as pd
+import math
 import matplotlib.pyplot as plt
 
-from mlfromscratch.utils.data_manipulation import train_test_split, normalize, to_categorical
-from mlfromscratch.utils.data_operation import accuracy_score
-from mlfromscratch.deep_learning.optimizers import GradientDescent, Adam
+from mlfromscratch.utils import train_test_split, normalize, to_categorical, accuracy_score
+from mlfromscratch.deep_learning.optimizers import Adam
 from mlfromscratch.deep_learning.loss_functions import CrossEntropy
 from mlfromscratch.deep_learning.activation_functions import Softmax
 from mlfromscratch.utils.kernels import *

mlfromscratch/examples/gradient_boosting_classifier.py

@@ -1,14 +1,11 @@
 from __future__ import division, print_function
 import numpy as np
 from sklearn import datasets
-import sys
-import os
 import matplotlib.pyplot as plt
 
 # Import helper functions
-from mlfromscratch.utils.data_manipulation import train_test_split
-from mlfromscratch.utils.data_operation import accuracy_score
-from mlfromscratch.utils.loss_functions import CrossEntropy
+from mlfromscratch.utils import train_test_split, accuracy_score
+from mlfromscratch.deep_learning.loss_functions import CrossEntropy
 from mlfromscratch.utils import Plot
 from mlfromscratch.supervised_learning import GradientBoostingClassifier
 

mlfromscratch/examples/gradient_boosting_regressor.py

@@ -1,18 +1,14 @@
 from __future__ import division, print_function
 import numpy as np
-from sklearn import datasets
 import pandas as pd
 import matplotlib.pyplot as plt
-from scipy.optimize import line_search
 import progressbar
 
-# Import helper functions
-from mlfromscratch.utils.data_manipulation import train_test_split, standardize, to_categorical
-from mlfromscratch.utils.data_operation import mean_squared_error, accuracy_score
+from mlfromscratch.utils import train_test_split, standardize, to_categorical
+from mlfromscratch.utils import mean_squared_error, accuracy_score, Plot
 from mlfromscratch.utils.loss_functions import SquareLoss
 from mlfromscratch.utils.misc import bar_widgets
 from mlfromscratch.supervised_learning import GradientBoostingRegressor
-from mlfromscratch.utils import Plot
 
 
 def main():

mlfromscratch/examples/k_means.py

@@ -1,8 +1,4 @@
 from __future__ import division, print_function
-import sys
-import os
-import math
-import random
 from sklearn import datasets
 import numpy as np
 

mlfromscratch/examples/k_nearest_neighbors.py

@@ -1,16 +1,10 @@
 from __future__ import print_function
-import sys
-import os
-import math
 import numpy as np
 import matplotlib.pyplot as plt
 from sklearn import datasets
 
-# Import helper functions
-from mlfromscratch.utils.data_manipulation import train_test_split, normalize
-from mlfromscratch.utils.data_operation import euclidean_distance, accuracy_score
-from mlfromscratch.unsupervised_learning import PCA
-from mlfromscratch.utils import Plot
+from mlfromscratch.utils import train_test_split, normalize, accuracy_score
+from mlfromscratch.utils import euclidean_distance, Plot
 from mlfromscratch.supervised_learning import KNN
 
 def main():

mlfromscratch/examples/linear_discriminant_analysis.py

@@ -1,17 +1,12 @@
 from __future__ import print_function
-import sys
-import os
 from sklearn import datasets
 import matplotlib.pyplot as plt
 import numpy as np
-import pandas as pd
 
-# Import helper functions
 from mlfromscratch.supervised_learning import LDA
-from mlfromscratch.utils.data_operation import calculate_covariance_matrix, accuracy_score
-from mlfromscratch.utils.data_manipulation import normalize, standardize, train_test_split
+from mlfromscratch.utils import calculate_covariance_matrix, accuracy_score
+from mlfromscratch.utils import normalize, standardize, train_test_split, Plot
 from mlfromscratch.unsupervised_learning import PCA
-from mlfromscratch.utils import Plot
 
 def main():
     # Load the dataset

mlfromscratch/examples/linear_regression.py

@@ -2,10 +2,8 @@
 import pandas as pd
 import matplotlib.pyplot as plt
 
-# Import helper functions
-from mlfromscratch.utils.data_manipulation import train_test_split, polynomial_features
-from mlfromscratch.utils.data_operation import mean_squared_error
-from mlfromscratch.utils import Plot
+from mlfromscratch.utils import train_test_split, polynomial_features
+from mlfromscratch.utils import mean_squared_error, Plot
 from mlfromscratch.supervised_learning import LinearRegression
 
 def main():

mlfromscratch/examples/logistic_regression.py

@@ -1,17 +1,11 @@
 from __future__ import print_function
-import sys
-import os
-import math
 from sklearn import datasets
 import numpy as np
-import pandas as pd
 import matplotlib.pyplot as plt
 
 # Import helper functions
-from mlfromscratch.utils.data_manipulation import make_diagonal, normalize, train_test_split
-from mlfromscratch.utils.data_operation import accuracy_score
-from mlfromscratch.utils.activation_functions import Sigmoid
-from mlfromscratch.utils.optimizers import GradientDescent
+from mlfromscratch.utils import make_diagonal, normalize, train_test_split, accuracy_score
+from mlfromscratch.deep_learning.activation_functions import Sigmoid
 from mlfromscratch.utils import Plot
 from mlfromscratch.supervised_learning import LogisticRegression
 
@@ -30,7 +24,6 @@ def main():
     y_pred = clf.predict(X_test)
 
     accuracy = accuracy_score(y_test, y_pred)
-
     print ("Accuracy:", accuracy)
 
     # Reduce dimension to two using PCA and plot the results