First commit

README.md

@@ -1,2 +1,35 @@
-# NeuralNetwork
+# N_Network
-Neural Network implementation based on the DeepLearning courses in Coursera
+
+Neural Network implementation based on the Andrew Ng courses
+
+Implements Batch GD, Stochastic GD (minibatch_size=1) & Stochastic minibatch GD:
+
+- Cost function: Cross Entropy Loss
+- Activation functions: relu, sigmoid, tanh
+- Regularization: l2 (lambd), Momentum (beta), Dropout (keep_prob)
+- Optimization: Minibatch Gradient Descent, RMS Prop, Adam
+- Learning rate decay, computes a factor of the learning rate at each # of epochs
+- Fair minibatches: Can create batches with the same proportion of labels 1/0 as in train data
+
+Restriction:
+
+- Multiclass only with onehot label
+
+## Install
+
+```bash
+pip install git+https://github.com/doctorado-ml/NeuralNetwork
+```
+
+## Example
+
+#### Console
+
+```bash
+python main.py
+```
+
+#### Jupyter Notebook
+
+[![Test](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Doctorado-ML/NeuralNetwork/blob/master/test.ipynb) Test notebook
+

main.py

@@ -0,0 +1,54 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import time
+from n_network import N_Network, plot_decision_boundary
+
+
+def load_planar_dataset(random_seed):
+    np.random.seed(random_seed)
+    m = 400 # number of examples
+    N = int(m / 2) # number of points per class
+    D = 2 # dimensionality
+    X = np.zeros((m,D)) # data matrix where each row is a single example
+    Y = np.zeros((m, 1), dtype='uint8') # labels vector (0 for red, 1 for blue)
+    a = 4 # maximum ray of the flower
+
+    for j in range(2):
+        ix = range(N * j, N * (j + 1))
+        t = np.linspace(j * 3.12, (j + 1) * 3.12, N) + np.random.randn(N) * 0.2 # theta
+        r = a * np.sin(4 * t) + np.random.randn(N) * 0.2 # radius
+        X[ix] = np.c_[r * np.sin(t), r * np.cos(t)]
+        Y[ix] = j
+        
+    X = X.T
+    Y = Y.T
+    return X, Y
+
+random_seed = 1
+Xtrain, ytrain = load_planar_dataset(random_seed)
+X = Xtrain.T
+y = ytrain.T
+print('X', X.shape, 'y', y.shape)
+
+# Visualize the data:
+plt.scatter(X[:, 0], X[:, 1], c=y.T[0], s=40, cmap=plt.cm.Spectral);
+plt.title('Dataset')
+plt.show();
+
+#Define a four layer network
+nu = [X.shape[1], 10, 7, 5, 1]
+xg = [0, N_Network.relu, N_Network.relu, N_Network.relu, N_Network.sigmoid]
+xgprime = [0, N_Network.relu_prime, N_Network.relu_prime, N_Network.relu_prime, N_Network.sigmoid_prime]
+init_params = dict(m=X.shape[0], n=X.shape[1], n_units=nu, g=xg, optim='sgd',
+                   gprime=xgprime, epochs=10000, alpha=0.075)
+nd = N_Network(init_params)
+nd.set_seed(random_seed)
+costs = nd.train(X, y)
+print("First cost: {0:.6f} final cost: {1:.6f}".format(costs[0], costs[-1]))
+print("Number of units in each layer: ", nu)
+nd.print_time()
+nd.plot_costs()
+pred = nd.valid(X, y)
+indices = nd.mislabeled(y, pred)
+# Plot decission boundary
+plot_decision_boundary(nd, X, y, True, '4 Layers N_Network')

n_network/Metrics.py

@@ -0,0 +1,220 @@
+'''
+__author__ = "Ricardo Montañana Gómez"
+__copyright__ = "Copyright 2020, Ricardo Montañana Gómez"
+__license__ = "MIT"
+Compute metrics for predicted data
+'''
+
+import numpy as np
+from .Utils import one_hot
+
+
+class Metrics:
+    """
+    True Positives (tp), These are the correctly predicted positive values
+    True Negatives (tn), These are the correctly predicted negative values
+    False Positives (fp), When actual class is target and predicted class is the other
+    False Negatives (fn), When actual class is reverse of target but predicted class is target
+    """
+    _truth = None
+    _predicted = None
+    _tp = None
+    _fp = None
+    _fn = None
+    _num_classes = 0
+
+    def __init__(self, y=None, yhat=None):
+        self._truth = self._adapt(y, update_num=True)
+        self._predicted = self._adapt(yhat)
+        self._compute_parameters()
+
+    def _adapt(self, data, update_num=False):
+        if data.max() > 1 or data.ndim == 1 or (data.ndim == 2 and data.shape[1] == 1):
+            if update_num:
+                self._num_classes = data.max() + 1
+            return data
+        else:
+            if update_num:
+                res = np.argmax(data, axis=1)
+                self._num_classes = res.max() + 1
+            return res
+
+    def _compute_param(self, set_a, set_b):
+        return np.sum(np.logical_and(set_a, set_b))
+
+    def _compute_parameters(self):
+
+        self._tp = np.zeros((self._num_classes), dtype=int)
+        self._fp = np.zeros((self._num_classes), dtype=int)
+        self._fn = np.zeros((self._num_classes), dtype=int)
+        for target in range(self._num_classes):
+            self._tp[target] = self._compute_param(
+                self._truth == target, self._predicted == target)
+            self._fp[target] = self._compute_param(
+                self._truth != target, self._predicted == target)
+            self._fn[target] = self._compute_param(
+                self._truth == target, self._predicted != target)
+
+    def parameters(self):
+        vmacro, vweigh, _, vmicro = self._compute_metrics()
+        return dict(tp=self._tp, fp=self._fp, fn=self._fn, macro=vmacro, weigh=vweigh, micro=vmicro)
+
+    def sets(self):
+        return self._truth, self._predicted
+
+    def fp_indices(self, target):
+        return np.where(np.logical_and(self._truth != target, self._predicted == target))[0]
+
+    def fn_indices(self, target):
+        return np.where(np.logical_and(self._truth == target, self._predicted != target))[0]
+
+    def correct(self):
+        """
+        Return the number of correct predictions
+        """
+        return np.sum(self._tp)
+
+    def _get_dict(self, vmacro, vweigh, vmicro):
+        return dict(macro=vmacro, weigh=vweigh, micro=vmicro)
+
+    def recall(self, target):
+        """
+        recall, Recall is the ratio of correctly predicted positive observations to the all observations in positive class
+        """
+        if target == 'all':
+            macro, weigh, _, micro = self._compute_metrics()
+            return self._get_dict(macro['rec'], weigh['rec'], micro['rec'])
+        else:
+            tp = self._tp[target]
+            fn = self._fn[target]
+            if (tp + fn) > 0:
+                return tp / (tp + fn)
+            return 0
+
+    def precision(self, target):
+        """
+        precision, Precision is the ratio of correctly predicted positive observations to the total predicted positive observations
+        """
+        if target == 'all':
+            macro, weigh, _, micro = self._compute_metrics()
+            return self._get_dict(macro['prec'], weigh['prec'], micro['prec'])
+        else:
+            tp = self._tp[target]
+            fp = self._fp[target]
+            if (tp + fp) > 0:
+                return tp / (tp + fp)
+            return 0
+
+    def accuracy(self):
+        """
+        accuracy, Accuracy is a ratio of correctly predicted observations to the total observations
+        """
+        tp = np.sum(self._tp)
+        elements = self._truth.size
+        if (elements) > 0:
+            return tp / elements
+        return 0
+
+    def f1(self, target):
+        """
+        f1 score, is the weighted average of Precision and Recall
+        """
+        if target == 'all':
+            macro, weigh, _, micro = self._compute_metrics()
+            return self._get_dict(macro['f1'], weigh['f1'], micro['f1'])
+        else:
+            divider = self.recall(target) + self.precision(target)
+            if divider != 0:
+                return 2 * (self.recall(target) * self.precision(target)) / divider
+            return 0
+
+    def confusion_matrix(self):
+        """
+        Return the confusion matrix associated to the data provided
+        """
+        result = np.zeros((self._num_classes, self._num_classes), dtype=int)
+        for target in reversed(range(self._num_classes)):
+            for j in range(self._num_classes):
+                result[target][j] = self._compute_param(
+                    self._truth == target, self._predicted == j)
+        return result
+
+    def debug(self):
+        for target in range(self._num_classes):
+            tp = self._tp[target]
+            fp = self._fp[target]
+            fn = self._fn[target]
+            print("target=[{0}], tp=[{1}], fp=[{2}], fn=[{3}]".format(
+                target, tp, fp, fn))
+            print("Truth shape=", self._truth.shape,
+                  " Prediction shape=", self._predicted.shape)
+            print("Number of classes:", self._num_classes)
+
+    def _compute_micro_metrics(self):
+        ttp = np.sum(self._tp)
+        tfp = np.sum(self._fp)
+        pr = re = ttp / (ttp + tfp)
+        if ttp + tfp == 0:
+            return 0
+        return 2 * (pr * re) / (pr + re), pr, re
+
+    def _compute_metrics(self):
+        tf1 = tpr = tre = 0.0
+        twf1 = twpr = twre = 0.0
+        total_samples = 0
+        for target in range(self._num_classes):
+            f1 = self.f1(target)
+            pr = self.precision(target)
+            re = self.recall(target)
+            num_samples = len(np.where(self._truth == target)[0])
+            tf1 += f1
+            tpr += pr
+            tre += re
+            twf1 += f1 * num_samples
+            twpr += pr * num_samples
+            twre += re * num_samples
+            total_samples += num_samples
+        tf1 /= self._num_classes
+        tpr /= self._num_classes
+        tre /= self._num_classes
+        twf1 /= total_samples
+        twpr /= total_samples
+        twre /= total_samples
+        mf1, mpr, mre = self._compute_micro_metrics()
+        macro = {}
+        weigh = {}
+        micro = {}
+        macro['f1'] = tf1
+        macro['prec'] = tpr
+        macro['rec'] = tre
+        weigh['f1'] = twf1
+        weigh['prec'] = twpr
+        weigh['rec'] = twre
+        micro['f1'] = mf1
+        micro['prec'] = mpr
+        micro['rec'] = mre
+        return macro, weigh, total_samples, micro
+
+    def classification_report(self, title='', digits=6):
+        def format_line(a, b, c, d, e):
+            return "[{0:^5}]\t[{1:.{digits}f}]\t[{2:.{digits}f}]\t[{3:.{digits}f}]\t[{4:5d}]".format(a, b, c, d, e, digits=digits)
+        print(
+            "======================== {0} ========================".format(title))
+
+        header = ['target', 'f1-score', 'precision', 'recall', 'support']
+        print("{d[0]:^7}\t{d[1]:^{length}.{length}}\t{d[2]:^{length}.{length}}\t{d[3]:^{length}.{length}}\t{d[4]:^7}".format(
+            d=header, length=digits + 4))
+        for target in range(self._num_classes):
+            f1 = self.f1(target)
+            pr = self.precision(target)
+            re = self.recall(target)
+            num_samples = len(np.where(self._truth == target)[0])
+            print(format_line(target, f1, pr, re, num_samples))
+        print("")
+        macro, weigh, total_samples, micro = self._compute_metrics()
+        print(format_line(
+            'macro', macro['f1'], macro['prec'], macro['rec'], total_samples))
+        print(format_line(
+            'weig.', weigh['f1'], weigh['prec'], weigh['rec'], total_samples))
+        print("accuracy=[{0:.{digits}f}]".format(
+            self.accuracy(), digits=digits))

n_network/Neural_Network.py

@@ -0,0 +1,540 @@
+'''
+__author__ = "Ricardo Montañana Gómez"
+__copyright__ = "Copyright 2020, Ricardo Montañana Gómez"
+__license__ = "MIT"
+Neural Network implementation based on the Andrew Ng courses
+Implements Batch GD, Stochastic GD (minibatch_size=1) & Stochastic minibatch GD:
+ -Cost function: Cross Entropy Loss
+ -Activation functions: relu, sigmoid, tanh
+ -Regularization: l2 (lambd), Momentum (beta), Dropout (keep_prob)
+ -Optimization: Minibatch Gradient Descent, RMS Prop, Adam
+ -Learning rate decay, computes a factor of the learning rate at each # of epochs
+ -Fair minibatches: Can create batches with the same proportion of labels 1/0 as in train data
+Restriction:
+ -Multiclass only with onehot label
+'''
+
+import time
+import math
+import pickle
+import numpy as np
+import matplotlib.pyplot as plt
+import seaborn as sns
+from .Metrics import Metrics
+
+
+# Cost function (Cross-entropy):
+# Compute the cross-entropy cost $J$
+# $$ J = -\frac{1}{m} \sum\limits_{i = 1}^{m} (y^{(i)}\log\left(a^{[L] (i)}\right) + (1 - y^{(i)})\log\left(1 - a^{[L](i)}\right)) \tag{7}$$
+
+
+class N_Network:
+    
+    def __init__(self, hyperparam):
+        # NN State
+        self._ct = 0  # Time inverted in computation
+        self._optim = {}  # Update parameters functions depending on the optimization algorithm
+        self._optim_update = None  # update function selected
+        self._optim_selected = ''
+        self._multiclass = False  # Is it a multiclass classification problem?
+        self._epochs_decay = ()  # (decay rate, applied each # epochs)
+        self._verbose = False
+        # Hyperparams
+        self._L = 0  # Number of layers including the input layer
+        self._n_units = []  # Number of units in each layer
+        self._g = []  # Activation functions of each layer
+        self._gprime = []  # Derivative of the activation functions needed in backpropagation
+        self._alpha = 0  # Learning rate in gradient descent
+        self._beta = 0  # Momentum coefficient / acts as beta1 in adam
+        self._beta2 = 0.999  # RMS Prop coefficient
+        self._epsilon = 1e-8  # RMS Prop value to prevent division by zero
+        self._params = {}  # dict of parameters
+        self._epochs = 0  # Number of iterations to train
+        self._seed = 2020  # Random seed
+        self._lambd = 0  # Regularization coefficient
+        self._keep_prob = 1  # dropout regularization
+        self._minibatch_size = 0  # Number of samples to take into account to upgrade parameters
+        self._fair_minibatches = False  # Wether or not create fair minibatches
+        if 'filename' in hyperparam:
+            self.load(hyperparam['filename'])
+            return
+        self._m = hyperparam['m']
+        self._n = hyperparam['n']
+        self._n_units = hyperparam['n_units']
+        self._g = hyperparam['g']
+        self._gprime = hyperparam['gprime']
+        self._alpha = hyperparam['alpha']
+        self._learning_rate = self._alpha
+        self._epochs = hyperparam['epochs']
+        self._L = len(self._n_units)
+        # ensures that at most, only one regularization method is chosen
+        if 'lambd' in hyperparam:
+            self._lambd = hyperparam['lambd']
+        else:
+            if 'keep_prob' in hyperparam:
+                self._keep_prob = hyperparam['keep_prob']
+        if 'minibatch_size' in hyperparam:
+            self._minibatch_size = hyperparam['minibatch_size']
+        else:
+            self._minibatch_size = self._m
+        if 'fair_minibatches' in hyperparam:
+            self._fair_minibatches = hyperparam['fair_minibatches']
+        optim = {
+            'adam': self._update_parameters_adam,
+            'sgd': self._update_parameters_sgd,
+            'rms': self._update_parameters_rms
+        }
+        self._optim_selected = hyperparam['optim']
+        self._optim_update = optim[self._optim_selected]
+        if hyperparam['optim'] != 'sgd':
+            self._beta = 0.9  # if opt. algorithm is rms or adam set default beta/beta1
+        if 'beta' in hyperparam:
+            self._beta = hyperparam['beta']
+        np.random.seed(self._seed)
+        if 'multiclass' in hyperparam:
+            self._multiclass = hyperparam['multiclass']
+        if 'epochs_decay' in hyperparam:
+            self._epochs_decay = hyperparam['epochs_decay']
+        self.initialize()
+
+    # Activation functions
+    @staticmethod
+    def softmax(x):  # stable softmax
+        exps = np.exp(x - np.max(x))
+        return exps / exps.sum(axis=0, keepdims=True)
+
+    @staticmethod
+    def softmax_prime(x):
+        return 1
+
+    @staticmethod
+    def relu(x):
+        return np.maximum(0, x)
+
+    @staticmethod
+    def sigmoid(x):
+        return 1 / (1 + np.exp(-x))
+
+    @staticmethod
+    def tanh(x):
+        return np.tanh(x)
+
+    @staticmethod
+    def sigmoid_prime(x):
+        s = N_Network.sigmoid(x)
+        return s * (1 - s)
+
+    @staticmethod
+    def relu_prime(x):
+        return np.greater(x, 0).astype(int)
+
+    @staticmethod
+    def tanh_prime(x):
+        z = N_Network.tanh(x)
+        return 1 - z * z
+
+    def initialize(self):
+        # Initialize dictionaries of Parameters
+        b = {}
+        W = {}
+        Z = {}
+        A = {}
+        dZ = {}
+        dW = {}
+        db = {}
+        vdW = {}
+        vdb = {}
+        SdW = {}
+        Sdb = {}
+        for i in range(self._L):
+            if self._verbose:
+                print("Initializing %d layer..." % i)
+            # Help ease the vanishing / Exploding gradient problem
+            cte = 0.01
+            if self._g[i] == self.relu:
+                # Make Var(W) = 2 / n
+                cte = np.sqrt(2 / self._n_units[i - 1])
+            else:
+                # based on Xavier initialization makes var(W) = 1 / n
+                if self._g[i] == self.tanh:
+                    cte = 1 / np.sqrt(self._n_units[i - 1])
+                else:
+                    # makes var(W) = 2 / n
+                    if self._g[i] == self.sigmoid:
+                        prev_layer = (i - 1) if i > 0 else 0
+                        cte = np.sqrt(
+                            2 / (self._n_units[prev_layer] + self._n_units[i]))
+            # Don't need W and b and its optimizers for the input layer
+            if i > 0:
+                W[i] = np.random.randn(
+                    self._n_units[i], self._n_units[i - 1]) * cte
+                b[i] = np.zeros((self._n_units[i], 1))
+                dW[i] = np.zeros(
+                    (self._n_units[i], self._n_units[i - 1] if i > 0 else self._minibatch_size))
+                db[i] = np.zeros((self._n_units[i], 1))
+                vdW[i] = np.zeros(
+                    (self._n_units[i], self._n_units[i - 1] if i > 0 else self._minibatch_size))
+                vdb[i] = np.zeros((self._n_units[i], 1))
+                SdW[i] = np.zeros(
+                    (self._n_units[i], self._n_units[i - 1] if i > 0 else self._minibatch_size))
+                Sdb[i] = np.zeros((self._n_units[i], 1))
+            A[i] = np.zeros(
+                (self._n_units[i], self._minibatch_size if i < self._L else 1))
+            Z[i] = np.zeros(
+                (self._n_units[i], self._minibatch_size if i < self._L else 1))
+            dZ[i] = np.zeros((self._n_units[i], self._minibatch_size))
+
+        self._params = dict(b=b, W=W, Z=Z, A=A, dZ=dZ, dW=dW,
+                            db=db, vdW=vdW, vdb=vdb, SdW=SdW, Sdb=Sdb)
+
+    def get_accuracy(self, y, ypred, direct_result=False):
+        m = y.shape[0]
+        met = Metrics(y, ypred)
+        ac = met.accuracy()
+        right = met.correct()
+        if direct_result:
+            return ac
+        return "Accuracy: {0:.3f}% ({1} of {2})".format(100 * ac, right, m)
+
+    def get_metrics(self, y, ypred):
+        return Metrics(y, ypred)
+
+    def plot_costs(self):
+        plt.plot(self._costs)
+        plt.ylabel('Cost (cross-entropy)')
+        plt.xlabel('Epochs')
+        plt.title("Epochs: {0} Learning rate: {1}".format(
+            self._epochs, self._learning_rate))
+        plt.show()
+
+    def plot_confusion_matrix(self, y, yhat, title='', figsize=(10, 7), scale=1.4):
+        cm = Metrics(y, yhat).confusion_matrix()
+        plt.figure(figsize=figsize)
+        sns.set(font_scale=scale)
+        fig = sns.heatmap(cm, annot=True, fmt='d', cmap="Blues", cbar=False)
+        x = fig.set_title("{0} ({1}) / {2}". format(title,
+                                                    self._optim_selected, self.get_accuracy(y, yhat)))
+        x = fig.set_xlabel('Predicted')
+        x = fig.set_ylabel('Truth')
+        # fig.invert_yaxis()
+
+    def check_dimensions(self):
+        for i in range(self._L):
+            print("i={0}, b({1}, W{2}, A{3}, Z{4}, vdW{5}, vdb{6}, SdW{7}, Sdb{8}, dW{9}, db{10}\n".format(
+                i, self._params['b'][i].shape if i > 0 else ' XXX',
+                self._params['W'][i].shape if i > 0 else ' XXX',
+                self._params['A'][i].shape,
+                self._params['Z'][i].shape,
+                self._params['vdW'][i].shape if i > 0 else ' XXX',
+                self._params['vdb'][i].shape if i > 0 else ' XXX',
+                self._params['SdW'][i].shape if i > 0 else ' XXX',
+                self._params['Sdb'][i].shape if i > 0 else ' XXX',
+                self._params['dW'][i].shape if i > 0 else ' XXX',
+                self._params['db'][i].shape if i > 0 else ' XXX'
+            ))
+
+    def get_params(self):
+        return self._params
+
+    def num_minibatches(self):
+        return math.floor(self._m / self._minibatch_size) + (0 if self._m % self._minibatch_size == 0 else 1)
+
+    def create_minibatches(self, X, y):
+        return self.create_fair_minibatches(X, y) if self._fair_minibatches else self.create_random_minibatches(X, y)
+
+    def _balance_sets(self, y):
+        """
+        Returns:
+        class0: category 0 indexes
+        class1: category 1 indexes 
+        num0: number of samples of 0 category to include in the minibatch
+        num1: number of samples of 1 category to include in the minibatch
+        """
+        class_one = np.array(np.where(y == 1))[0]
+        class_zero = np.array(np.where(y == 0))[0]
+        percent = len(class_one) / len(y)
+        num_class0 = math.floor((1 - percent) * self._minibatch_size)
+        num_class1 = self._minibatch_size - num_class0
+        return num_class0, num_class1, class_zero, class_one
+
+    def create_fair_minibatches(self, X, y):
+        """
+        Creates a list of random minibatches from (X, y) 
+
+        """
+        mini_batches = []
+        num_zero, num_one, class_zero, class_one = self._balance_sets(y)
+        # Compute categorized shuffled sets
+        X0 = X[class_zero]
+        X1 = X[class_one]
+        y0 = y[class_zero]
+        y1 = y[class_one]
+        permutation0 = list(np.random.permutation(len(class_zero)))
+        permutation1 = list(np.random.permutation(len(class_one)))
+        shuffledX0 = X0[permutation0, :]
+        shuffledX1 = X1[permutation1, :]
+        shuffledY0 = y0[permutation0, :]
+        shuffledY1 = y1[permutation1, :]
+        size = self._minibatch_size
+
+        num = math.floor(self._m / size)
+        for k in range(num):
+            # Inserts the category 0 elements to mini batch
+            miniX = shuffledX0[k * num_zero:(k + 1) * num_zero, :]
+            miniY = shuffledY0[k * num_zero:(k + 1) * num_zero, :]
+            # Appends the cateogory 1 elements to mini batch
+            miniX = np.vstack((miniX, X1[k * num_one:(k + 1) * num_one, :]))
+            miniY = np.vstack((miniY, y1[k * num_one:(k + 1) * num_one, :]))
+            mini_batch = (miniX, miniY)
+            mini_batches.append(mini_batch)
+        if self._m % num != 0:
+            miniX = shuffledX0[num * num_zero:y0.shape[0], :]
+            miniY = shuffledY0[num * num_zero:y0.shape[0], :]
+            miniX = np.vstack((miniX, X1[num * num_one:y1.shape[0], :]))
+            miniY = np.vstack((miniY, y1[num * num_one:y1.shape[0], :]))
+            mini_batch = (miniX, miniY)
+            mini_batches.append(mini_batch)
+        return mini_batches
+
+    def create_random_minibatches(self, X, y):
+        """
+        Creates a list of random minibatches from (X, y) 
+
+        """
+        mini_batches = []
+        permutation = list(np.random.permutation(self._m))
+        shuffledX = X[permutation, :]
+        shuffledY = y[permutation, :]
+        size = self._minibatch_size
+        num = math.floor(self._m / size)
+        for k in range(num):
+            miniX = shuffledX[k * size:(k + 1) * size, :]
+            miniY = shuffledY[k * size:(k + 1) * size, :]
+            mini_batch = (miniX, miniY)
+            mini_batches.append(mini_batch)
+        if self._m % size != 0:
+            miniX = shuffledX[num * size:self._m, :]
+            miniY = shuffledY[num * size:self._m, :]
+            mini_batch = (miniX, miniY)
+            mini_batches.append(mini_batch)
+        return mini_batches
+
+    def _compute_Sd(self, i):
+        self._params['SdW'][i] = self._beta2 * self._params['SdW'][i] + \
+            (1 - self._beta2) * np.square(self._params['dW'][i])
+        self._params['Sdb'][i] = self._beta2 * self._params['Sdb'][i] + \
+            (1 - self._beta2) * np.square(self._params['db'][i])
+        return self._params['SdW'][i], self._params['Sdb'][i]
+
+    def _compute_vd(self, i):
+        self._params['vdW'][i] = self._beta * self._params['vdW'][i] + \
+            (1 - self._beta) * self._params['dW'][i]
+        self._params['vdb'][i] = self._beta * self._params['vdb'][i] + \
+            (1 - self._beta) * self._params['db'][i]
+        return self._params['vdW'][i], self._params['vdb'][i]
+
+    def _update_parameters_rms(self, t):
+        for i in range(1, self._L):
+            SdW, Sdb = self._compute_Sd(i)
+            dW = self._params['dW'][i]
+            db = self._params['db'][i]
+            self._params['W'][i] -= self._alpha * \
+                dW / (np.sqrt(SdW) + self._epsilon)
+            self._params['b'][i] -= self._alpha * \
+                db / (np.sqrt(Sdb) + self._epsilon)
+
+    def _update_parameters_adam(self, t):
+        for i in range(1, self._L):
+            vdW, vdb = self._compute_vd(i)
+            SdW, Sdb = self._compute_Sd(i)
+            vdW_corr = vdW / (1 - math.pow(self._beta, 2))
+            vdb_corr = vdb / (1 - math.pow(self._beta, 2))
+            SdW_corr = SdW / (1 - math.pow(self._beta2, t))
+            Sdb_corr = Sdb / (1 - math.pow(self._beta2, t))
+            self._params['W'][i] -= self._alpha * \
+                vdW_corr / (np.sqrt(SdW_corr) + self._epsilon)
+            self._params['b'][i] -= self._alpha * \
+                vdb_corr / (np.sqrt(Sdb_corr) + self._epsilon)
+
+    def _update_parameters_sgd(self, t):
+        for i in range(1, self._L):
+            vdW, vdb = self._compute_vd(i)
+            self._params['W'][i] -= self._alpha * vdW
+            self._params['b'][i] -= self._alpha * vdb
+
+    def set_verbose(self, verbose):
+        self._verbose = verbose
+
+    def set_seed(self, seed):
+        self._seed = seed
+        np.random.seed(self._seed)
+
+    def _cost_function(self, yhat, y):
+        """
+        Compute cost (cross-entropy) of prediction
+
+        yhat: vector of predictions, shape (number of examples, 1)
+        Y:  vector of labels, shape (number of examples, 1)
+
+        Returns: cost
+        """
+        if self._multiclass:
+            cost = -np.mean(y * np.log(yhat + self._epsilon))
+        else:
+            cost = -np.sum(np.nansum(y * np.log(yhat) + (1 - y)
+                                     * np.log(1 - yhat))) / self._minibatch_size
+        # Add regularization term
+        cost += self._lambd / (2 * self._minibatch_size) * \
+            np.sum([np.sum(np.square(x)) for x in self._params['W']])
+        assert(cost.shape == ())
+        return cost
+
+    def _get_prediction(self, transform=False):
+        res = self._get_AL().T
+        if transform:
+            if self._multiclass:
+                return np.argmax(res, axis=1)
+            else:
+                return np.round(res).astype(int)
+        return res
+
+    def _get_AL(self):
+        return self._params['A'][self._L - 1]
+
+    def _backward_propagation(self, y):
+        AL = self._get_AL()
+        Y = y.T
+        assert(Y.shape == AL.shape)
+        if self._multiclass:
+            dA = AL - Y
+        else:
+            # derivative of cost with respect to A[L]
+            dA = np.nan_to_num(-(np.divide(Y, AL) - np.divide(1 - Y, 1 - AL)))
+        for i in reversed(range(1, self._L)):
+            dZ = dA * self._gprime[i](self._params['Z'][i])
+            dW = dZ.dot(self._params['A'][i - 1].T) / self._minibatch_size + \
+                (self._lambd / self._minibatch_size) * self._params['W'][i]
+            db = np.sum(dZ, axis=1, keepdims=True) / self._minibatch_size
+            dA = self._params['W'][i].T.dot(dZ)
+            self._params['dW'][i] = dW
+            self._params['db'][i] = db
+
+    def train(self, X, y):
+        return self.fit(X, y)
+
+    def fit(self, X, y):
+        self._costs = []
+        tic = time.time()
+        if self._verbose:
+            print('Training neural net...{0} epochs with {1} minibatches'.format(
+                self._epochs, self.num_minibatches()))
+        divider = 1 if self._epochs < 100 else 100
+        t = 0
+        for e in range(self._epochs):
+            minibatches = self.create_minibatches(X, y)
+            cost_total = 0
+            for minibatch in minibatches:
+                Xt, yt = minibatch
+                self._forward_propagation(Xt, train=True)
+                # Compute gradient descent
+                self._backward_propagation(yt)
+                t += 1  # Only used in adam
+                self._optim_update(t)
+                cost_total += self._cost_function(self._get_prediction(), yt)
+            cost_avg = cost_total / self.num_minibatches()
+            self._costs.append(cost_avg)
+            if e % divider == 0 and self._verbose:
+                print("Epoch: {0} Cost {1:.8f}".format(e, cost_avg))
+            if self._epochs_decay != ():
+                (rate, number) = self._epochs_decay
+                if e > 0 and e % number == 0:
+                    self._alpha *= rate
+                    if self._verbose:
+                        print(
+                            "*Setting learning rate (alpha) to: {0}".format(self._alpha))
+        self._ct = time.time() - tic
+        self._alpha = self._learning_rate
+        if self._verbose:
+            self.print_time()
+        return self._costs
+
+    def print_time(self):
+        print("Elapsed time: {0:.2f} s".format(self._ct))
+
+    def _forward_propagation(self, X, train=False):
+        self._params['A'][0] = X.T
+        for i in range(1, self._L):
+            if train and self._keep_prob != 1:
+                d = np.random.rand(*self._params['A'][i].shape)
+                d = (d < self._keep_prob).astype(int)
+                '''
+                 divide by self._keep_prob is done to keep the same behavior of the neuron in training with dropout and in
+                 testing without dropout. "This is important because at test time all neurons see all their inputs, 
+                 so we want the outputs of neurons at test time to be identical to their expected outputs at training time"
+                 (Stanford CS231n Convolutional Neural Networks for Visual Recognition)
+                '''
+                self._params['A'][i] = (
+                    self._params['A'][i] * d) / self._keep_prob  # inverted dropout
+            self._params['Z'][i] = self._params['W'][i].dot(
+                self._params['A'][i - 1]) + self._params['b'][i]
+            self._params['A'][i] = self._g[i](self._params['Z'][i])
+        prediction = self._get_AL()
+
+    def predict(self, X):
+        self._forward_propagation(X, train=False)
+        if self._multiclass:
+            yhat = np.argmax(self._get_prediction(False), axis=1)
+        else:
+            yhat = self._get_prediction(transform=True)
+        return yhat
+
+    def predict_proba(self, X):
+        self._forward_propagation(X, train=False)
+        return self._get_prediction(transform=False)
+
+    def evaluate(self, X, y, transform=True):
+        return self.valid(X, y, transform)
+
+    def valid(self, X, y, transform=True, score=False):
+        if X.shape[0] != y.shape[0]:
+            print('Dimension error X, y', X.shape, y.shape)
+        yhat = self.predict(X)
+        ypred = self._get_prediction(transform=True)
+        if score:
+            return self.get_accuracy(y, ypred, direct_result=True)
+        print(self.get_accuracy(y, ypred))
+        return yhat
+
+    def score(self, X, y):
+        return self.valid(X, y, score=True)
+
+    def mislabeled(self, y, ypred, target=1):
+        return Metrics(y, ypred).fn_indices(target)
+
+    def save(self, name=''):
+        try:
+            filename = "{0}.nn".format(name)
+            f = open(filename, 'wb')
+            pickle.dump(self.__dict__, f, 2)
+            f.close()
+        except:
+            print("I couldn't write the file ", filename)
+            return False
+        return True
+
+    def load(self, filename):
+        try:
+            f = open(filename, 'rb')
+            tmp_dict = pickle.load(f)
+            f.close()
+        except:
+            print(filename, " doesn't exists or I couldn't open it.")
+            return False
+        self.__dict__.update(tmp_dict)
+        return True
+
+    def compact_state(self):
+        return {
+            "_m": self._m,
+            "_n": self._n
+        }

n_network/Utils.py

@@ -0,0 +1,44 @@
+'''
+__author__ = "Ricardo Montañana Gómez"
+__copyright__ = "Copyright 2020, Ricardo Montañana Gómez"
+__license__ = "MIT"
+Util functions to use with the classifier
+'''
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+
+def one_hot(label, num):
+    yht = np.zeros((label.size, num))
+    yht[np.arange(label.size), label.T] = 1
+    return yht
+
+
+def plot_decision_boundary(model, X, y, binary, title):
+    y = y.T[0]
+    # Set min and max values and give it some padding
+    x_min, x_max = X[:, 0].min() - 1, X[:, 0].max() + 1
+    y_min, y_max = X[:, 1].min() - 1, X[:, 1].max() + 1
+    h = 0.01
+    # Generate a grid of points with distance h between them
+    xx, yy = np.meshgrid(np.arange(x_min, x_max, h),
+                         np.arange(y_min, y_max, h))
+    # Predict the function value for the whole grid
+    case = np.array(np.c_[xx.ravel(), yy.ravel()])
+    if type(model).__name__ == 'N_Network':
+        if binary:
+            Z = model.predict(case)
+        else:
+            Z = model.predict_proba(case)
+    else:
+        Z = model.predict(case)
+        Z = np.round(Z) if binary else Z
+    Z = Z.reshape(xx.shape)
+    # Plot the contour and training examples
+    plt.title(title + ' Decision boundary')
+    plt.contourf(xx, yy, Z, cmap=plt.cm.Spectral)
+    plt.ylabel('x2')
+    plt.xlabel('x1')
+    plt.scatter(X[:, 0], X[:, 1], c=y, cmap=plt.cm.Spectral)
+    plt.show()

n_network/__init__.py

@@ -0,0 +1,3 @@
+from .Neural_Network import N_Network
+from .Metrics import Metrics
+from .Utils import plot_decision_boundary, one_hot

requirements.txt

@@ -0,0 +1,5 @@
+numpy
+scikit-learn
+matplotlib
+seaborn
+git+https://github.com/doctorado-ml/stree

setup.py

@@ -0,0 +1,38 @@
+import setuptools
+
+__version__ = "1.0rc1"
+__author__ = "Ricardo Montañana Gómez"
+
+def readme():
+    with open('README.md') as f:
+        return f.read()
+
+
+setuptools.setup(
+    name='N_Network',
+    version=__version__,
+    license='MIT License',
+    description='A personal implementation of a Neural Network',
+    long_description=readme(),
+    long_description_content_type='text/markdown',
+    packages=setuptools.find_packages(),
+    url='https://github.com/doctorado-ml/neuralnetwork',
+    author=__author__,
+    author_email='ricardo.montanana@alu.uclm.es',
+    keywords='neural_network',
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3.7',
+        'Natural Language :: English',
+        'Topic :: Scientific/Engineering :: Artificial Intelligence',
+        'Intended Audience :: Science/Research'
+    ],
+    install_requires=[
+        'scikit-learn>=0.23.0',
+        'numpy',
+        'matplotlib',
+        'seaborn'
+    ],
+    zip_safe=False
+)