deep_learning4e.py

"""Deep learning. (Chapters 20)"""

import random
import statistics

import numpy as np
from keras import Sequential, optimizers
from keras.layers import Embedding, SimpleRNN, Dense
from keras.preprocessing import sequence

from utils4e import (conv1D, gaussian_kernel, element_wise_product, vector_add, random_weights,
                     scalar_vector_product, map_vector, mean_squared_error_loss)


class Node:
    """
    A single unit of a layer in a neural network
    :param weights: weights between parent nodes and current node
    :param value: value of current node
    """

    def __init__(self, weights=None, value=None):
        self.value = value
        self.weights = weights or []


class Layer:
    """
    A layer in a neural network based on a computational graph.
    :param size: number of units in the current layer
    """

    def __init__(self, size):
        self.nodes = np.array([Node() for _ in range(size)])

    def forward(self, inputs):
        """Define the operation to get the output of this layer"""
        raise NotImplementedError


class Activation:

    def function(self, x):
        return NotImplementedError

    def derivative(self, x):
        return NotImplementedError

    def __call__(self, x):
        return self.function(x)


class Sigmoid(Activation):

    def function(self, x):
        return 1 / (1 + np.exp(-x))

    def derivative(self, value):
        return value * (1 - value)


class ReLU(Activation):

    def function(self, x):
        return max(0, x)

    def derivative(self, value):
        return 1 if value > 0 else 0


class ELU(Activation):

    def __init__(self, alpha=0.01):
        self.alpha = alpha

    def function(self, x):
        return x if x > 0 else self.alpha * (np.exp(x) - 1)

    def derivative(self, value):
        return 1 if value > 0 else self.alpha * np.exp(value)


class LeakyReLU(Activation):

    def __init__(self, alpha=0.01):
        self.alpha = alpha

    def function(self, x):
        return max(x, self.alpha * x)

    def derivative(self, value):
        return 1 if value > 0 else self.alpha


class Tanh(Activation):

    def function(self, x):
        return np.tanh(x)

    def derivative(self, value):
        return 1 - (value ** 2)


class SoftMax(Activation):

    def function(self, x):
        return np.exp(x) / np.sum(np.exp(x))

    def derivative(self, x):
        return np.ones_like(x)


class SoftPlus(Activation):

    def function(self, x):
        return np.log(1. + np.exp(x))

    def derivative(self, x):
        return 1. / (1. + np.exp(-x))


class Linear(Activation):

    def function(self, x):
        return x

    def derivative(self, x):
        return np.ones_like(x)


class InputLayer(Layer):
    """1D input layer. Layer size is the same as input vector size."""

    def __init__(self, size=3):
        super().__init__(size)

    def forward(self, inputs):
        """Take each value of the inputs to each unit in the layer."""
        assert len(self.nodes) == len(inputs)
        for node, inp in zip(self.nodes, inputs):
            node.value = inp
        return inputs


class OutputLayer(Layer):
    """1D softmax output layer in 19.3.2."""

    def __init__(self, size=3):
        super().__init__(size)

    def forward(self, inputs, activation=SoftMax):
        assert len(self.nodes) == len(inputs)
        res = activation().function(inputs)
        for node, val in zip(self.nodes, res):
            node.value = val
        return res


class DenseLayer(Layer):
    """
    1D dense layer in a neural network.
    :param in_size: (int) input vector size
    :param out_size: (int) output vector size
    :param activation: (Activation object) activation function
    """

    def __init__(self, in_size=3, out_size=3, activation=Sigmoid):
        super().__init__(out_size)
        self.out_size = out_size
        self.inputs = None
        self.activation = activation()
        # initialize weights
        for node in self.nodes:
            node.weights = random_weights(-0.5, 0.5, in_size)

    def forward(self, inputs):
        self.inputs = inputs
        res = []
        # get the output value of each unit
        for unit in self.nodes:
            val = self.activation.function(np.dot(unit.weights, inputs))
            unit.value = val
            res.append(val)
        return res


class ConvLayer1D(Layer):
    """
    1D convolution layer of in neural network.
    :param kernel_size: convolution kernel size
    """

    def __init__(self, size=3, kernel_size=3):
        super().__init__(size)
        # init convolution kernel as gaussian kernel
        for node in self.nodes:
            node.weights = gaussian_kernel(kernel_size)

    def forward(self, features):
        # each node in layer takes a channel in the features
        assert len(self.nodes) == len(features)
        res = []
        # compute the convolution output of each channel, store it in node.val
        for node, feature in zip(self.nodes, features):
            out = conv1D(feature, node.weights)
            res.append(out)
            node.value = out
        return res


class MaxPoolingLayer1D(Layer):
    """
    1D max pooling layer in a neural network.
    :param kernel_size: max pooling area size
    """

    def __init__(self, size=3, kernel_size=3):
        super().__init__(size)
        self.kernel_size = kernel_size
        self.inputs = None

    def forward(self, features):
        assert len(self.nodes) == len(features)
        res = []
        self.inputs = features
        # do max pooling for each channel in features
        for i in range(len(self.nodes)):
            feature = features[i]
            # get the max value in a kernel_size * kernel_size area
            out = [max(feature[i:i + self.kernel_size])
                   for i in range(len(feature) - self.kernel_size + 1)]
            res.append(out)
            self.nodes[i].value = out
        return res


class BatchNormalizationLayer(Layer):
    """Batch normalization layer."""

    def __init__(self, size, eps=0.001):
        super().__init__(size)
        self.eps = eps
        # self.weights = [beta, gamma]
        self.weights = [0, 0]
        self.inputs = None

    def forward(self, inputs):
        # mean value of inputs
        mu = sum(inputs) / len(inputs)
        # standard error of inputs
        stderr = statistics.stdev(inputs)
        self.inputs = inputs
        res = []
        # get normalized value of each input
        for i in range(len(self.nodes)):
            val = [(inputs[i] - mu) * self.weights[0] / np.sqrt(self.eps + stderr ** 2) + self.weights[1]]
            res.append(val)
            self.nodes[i].value = val
        return res


def init_examples(examples, idx_i, idx_t, o_units):
    """Init examples from dataset.examples."""

    inputs, targets = {}, {}
    for i, e in enumerate(examples):
        # input values of e
        inputs[i] = [e[i] for i in idx_i]

        if o_units > 1:
            # one-hot representation of e's target
            t = [0 for i in range(o_units)]
            t[e[idx_t]] = 1
            targets[i] = t
        else:
            # target value of e
            targets[i] = [e[idx_t]]

    return inputs, targets


def stochastic_gradient_descent(dataset, net, loss, epochs=1000, l_rate=0.01, batch_size=1, verbose=False):
    """
    Gradient descent algorithm to update the learnable parameters of a network.
    :return: the updated network
    """
    examples = dataset.examples  # init data

    for e in range(epochs):
        total_loss = 0
        random.shuffle(examples)
        weights = [[node.weights for node in layer.nodes] for layer in net]

        for batch in get_batch(examples, batch_size):
            inputs, targets = init_examples(batch, dataset.inputs, dataset.target, len(net[-1].nodes))
            # compute gradients of weights
            gs, batch_loss = BackPropagation(inputs, targets, weights, net, loss)
            # update weights with gradient descent
            weights = [x + y for x, y in zip(weights, [np.array(tg) * -l_rate for tg in gs])]
            total_loss += batch_loss

            # update the weights of network each batch
            for i in range(len(net)):
                if weights[i].size != 0:
                    for j in range(len(weights[i])):
                        net[i].nodes[j].weights = weights[i][j]

        if verbose:
            print("epoch:{}, total_loss:{}".format(e + 1, total_loss))

    return net


def adam(dataset, net, loss, epochs=1000, rho=(0.9, 0.999), delta=1 / 10 ** 8,
         l_rate=0.001, batch_size=1, verbose=False):
    """
    [Figure 19.6]
    Adam optimizer to update the learnable parameters of a network.
    Required parameters are similar to gradient descent.
    :return the updated network
    """
    examples = dataset.examples

    # init s,r and t
    s = [[[0] * len(node.weights) for node in layer.nodes] for layer in net]
    r = [[[0] * len(node.weights) for node in layer.nodes] for layer in net]
    t = 0

    # repeat util converge
    for e in range(epochs):
        # total loss of each epoch
        total_loss = 0
        random.shuffle(examples)
        weights = [[node.weights for node in layer.nodes] for layer in net]

        for batch in get_batch(examples, batch_size):
            t += 1
            inputs, targets = init_examples(batch, dataset.inputs, dataset.target, len(net[-1].nodes))

            # compute gradients of weights
            gs, batch_loss = BackPropagation(inputs, targets, weights, net, loss)

            # update s,r,s_hat and r_gat
            s = vector_add(scalar_vector_product(rho[0], s),
                           scalar_vector_product((1 - rho[0]), gs))
            r = vector_add(scalar_vector_product(rho[1], r),
                           scalar_vector_product((1 - rho[1]), element_wise_product(gs, gs)))
            s_hat = scalar_vector_product(1 / (1 - rho[0] ** t), s)
            r_hat = scalar_vector_product(1 / (1 - rho[1] ** t), r)

            # rescale r_hat
            r_hat = map_vector(lambda x: 1 / (np.sqrt(x) + delta), r_hat)

            # delta weights
            delta_theta = scalar_vector_product(-l_rate, element_wise_product(s_hat, r_hat))
            weights = vector_add(weights, delta_theta)
            total_loss += batch_loss

            # update the weights of network each batch
            for i in range(len(net)):
                if weights[i]:
                    for j in range(len(weights[i])):
                        net[i].nodes[j].weights = weights[i][j]

        if verbose:
            print("epoch:{}, total_loss:{}".format(e + 1, total_loss))

    return net


def BackPropagation(inputs, targets, theta, net, loss):
    """
    The back-propagation algorithm for multilayer networks in only one epoch, to calculate gradients of theta.
    :param inputs: a batch of inputs in an array. Each input is an iterable object
    :param targets: a batch of targets in an array. Each target is an iterable object
    :param theta: parameters to be updated
    :param net: a list of predefined layer objects representing their linear sequence
    :param loss: a predefined loss function taking array of inputs and targets
    :return: gradients of theta, loss of the input batch
    """

    assert len(inputs) == len(targets)
    o_units = len(net[-1].nodes)
    n_layers = len(net)
    batch_size = len(inputs)

    gradients = [[[] for _ in layer.nodes] for layer in net]
    total_gradients = [[[0] * len(node.weights) for node in layer.nodes] for layer in net]

    batch_loss = 0

    # iterate over each example in batch
    for e in range(batch_size):
        i_val = inputs[e]
        t_val = targets[e]

        # forward pass and compute batch loss
        for i in range(1, n_layers):
            layer_out = net[i].forward(i_val)
            i_val = layer_out
        batch_loss += loss(t_val, layer_out)

        # initialize delta
        delta = [[] for _ in range(n_layers)]

        previous = np.array([layer_out[i] - t_val[i] for i in range(o_units)])
        h_layers = n_layers - 1

        # backward pass
        for i in range(h_layers, 0, -1):
            layer = net[i]
            derivative = np.array([layer.activation.derivative(node.value) for node in layer.nodes])
            delta[i] = previous * derivative
            # pass to layer i-1 in the next iteration
            previous = np.matmul([delta[i]], theta[i])[0]
            # compute gradient of layer i
            gradients[i] = [scalar_vector_product(d, net[i].inputs) for d in delta[i]]

        # add gradient of current example to batch gradient
        total_gradients = vector_add(total_gradients, gradients)

    return total_gradients, batch_loss


def get_batch(examples, batch_size=1):
    """Split examples into multiple batches"""
    for i in range(0, len(examples), batch_size):
        yield examples[i: i + batch_size]


class NeuralNetworkLearner:
    """
    Simple dense multilayer neural network.
    :param hidden_layer_sizes: size of hidden layers in the form of a list
    """

    def __init__(self, dataset, hidden_layer_sizes, l_rate=0.01, epochs=1000, batch_size=10,
                 optimizer=stochastic_gradient_descent, loss=mean_squared_error_loss, verbose=False, plot=False):
        self.dataset = dataset
        self.l_rate = l_rate
        self.epochs = epochs
        self.batch_size = batch_size
        self.optimizer = optimizer
        self.loss = loss
        self.verbose = verbose
        self.plot = plot

        input_size = len(dataset.inputs)
        output_size = len(dataset.values[dataset.target])

        # initialize the network
        raw_net = [InputLayer(input_size)]
        # add hidden layers
        hidden_input_size = input_size
        for h_size in hidden_layer_sizes:
            raw_net.append(DenseLayer(hidden_input_size, h_size))
            hidden_input_size = h_size
        raw_net.append(DenseLayer(hidden_input_size, output_size))
        self.raw_net = raw_net

    def fit(self, X, y):
        self.learned_net = self.optimizer(self.dataset, self.raw_net, loss=self.loss, epochs=self.epochs,
                                          l_rate=self.l_rate, batch_size=self.batch_size, verbose=self.verbose)
        return self

    def predict(self, example):
        n_layers = len(self.learned_net)

        layer_input = example
        layer_out = example

        # get the output of each layer by forward passing
        for i in range(1, n_layers):
            layer_out = self.learned_net[i].forward(np.array(layer_input).reshape((-1, 1)))
            layer_input = layer_out

        return layer_out.index(max(layer_out))


class PerceptronLearner:
    """
    Simple perceptron neural network.
    """

    def __init__(self, dataset, l_rate=0.01, epochs=1000, batch_size=10, optimizer=stochastic_gradient_descent,
                 loss=mean_squared_error_loss, verbose=False, plot=False):
        self.dataset = dataset
        self.l_rate = l_rate
        self.epochs = epochs
        self.batch_size = batch_size
        self.optimizer = optimizer
        self.loss = loss
        self.verbose = verbose
        self.plot = plot

        input_size = len(dataset.inputs)
        output_size = len(dataset.values[dataset.target])

        # initialize the network, add dense layer
        self.raw_net = [InputLayer(input_size), DenseLayer(input_size, output_size)]

    def fit(self, X, y):
        self.learned_net = self.optimizer(self.dataset, self.raw_net, loss=self.loss, epochs=self.epochs,
                                          l_rate=self.l_rate, batch_size=self.batch_size, verbose=self.verbose)
        return self

    def predict(self, example):
        layer_out = self.learned_net[1].forward(np.array(example).reshape((-1, 1)))
        return layer_out.index(max(layer_out))


def keras_dataset_loader(dataset, max_length=500):
    """
    Helper function to load keras datasets.
    :param dataset: keras data set type
    :param max_length: max length of each input sequence
    """
    # init dataset
    (X_train, y_train), (X_val, y_val) = dataset
    if max_length > 0:
        X_train = sequence.pad_sequences(X_train, maxlen=max_length)
        X_val = sequence.pad_sequences(X_val, maxlen=max_length)
    return (X_train[10:], y_train[10:]), (X_val, y_val), (X_train[:10], y_train[:10])


def SimpleRNNLearner(train_data, val_data, epochs=2, verbose=False):
    """
    RNN example for text sentimental analysis.
    :param train_data: a tuple of (training data, targets)
            Training data: ndarray taking training examples, while each example is coded by embedding
            Targets: ndarray taking targets of each example. Each target is mapped to an integer
    :param val_data: a tuple of (validation data, targets)
    :param epochs: number of epochs
    :param verbose: verbosity mode
    :return: a keras model
    """

    total_inputs = 5000
    input_length = 500

    # init data
    X_train, y_train = train_data
    X_val, y_val = val_data

    # init a the sequential network (embedding layer, rnn layer, dense layer)
    model = Sequential()
    model.add(Embedding(total_inputs, 32, input_length=input_length))
    model.add(SimpleRNN(units=128))
    model.add(Dense(1, activation='sigmoid'))
    model.compile(loss='binary_crossentropy', optimizer='adam', metrics=['accuracy'])

    # train the model
    model.fit(X_train, y_train, validation_data=(X_val, y_val), epochs=epochs, batch_size=128, verbose=verbose)

    return model


def AutoencoderLearner(inputs, encoding_size, epochs=200, verbose=False):
    """
    Simple example of linear auto encoder learning producing the input itself.
    :param inputs: a batch of input data in np.ndarray type
    :param encoding_size: int, the size of encoding layer
    :param epochs: number of epochs
    :param verbose: verbosity mode
    :return: a keras model
    """

    # init data
    input_size = len(inputs[0])

    # init model
    model = Sequential()
    model.add(Dense(encoding_size, input_dim=input_size, activation='relu', kernel_initializer='random_uniform',
                    bias_initializer='ones'))
    model.add(Dense(input_size, activation='relu', kernel_initializer='random_uniform', bias_initializer='ones'))

    # update model with sgd
    sgd = optimizers.SGD(lr=0.01)
    model.compile(loss='mean_squared_error', optimizer=sgd, metrics=['accuracy'])

    # train the model
    model.fit(inputs, inputs, epochs=epochs, batch_size=10, verbose=verbose)

    return model