Multi-Layer Deep Neural Network from Scratch in Python


  • TOC {:toc}

Let's write a multi layer deep neural network from scratch in Python. But why do we need to write neural network from scratch while there are already tools like Keras? It is a good exercise as well as refreshment of the knowledge about how neural networks works. For neural network from scratch, we need to have some knowledge of Calculus, Linear Algebra, OOP (here in this blog).

I am not using <i>gist</i> for codes, so don't panic if you find unfriendly text formats. Also I have written this blog on Markdown of Jupyter Notebook so the formats are a bit different. But the truth is, the class we will be building will be just like keras. Yes Keras!


  • 2020/05/29: Published blog.
  • 2022/11/10: Fixed errors in derivative.

1.1 What I am covering on this blog?

  • Honestly, a scary and another blog about writing a Neural Network from scratch but I am leaving all the complex mathematics(also giving links to them at last).
  • This blog will also act as <b>prerequisites concept for Convolutional Neural Network from scratch</b> which I will write on next blog.
  • Doing MNIST classification using softmax cross entropy and GD` optimizer.
  • Saving and loading model.

For this code, I will be using:

  • numpy
  • matplotlib for plotting
  • pandas for just summary
  • time for viewing time

2. Warning

<b>I am not going to make next Keras or Tensorflow here.</b> This is only going to be simple multi layer neural network from scratch.

Most of these days, we have many ML frameworks with many choices. We have high level to low level frameworks. Recently PyTorch has earned huge popularity but for beginners, Keras is a best choice. But writing a ML code and neural network from scratch is always a challenging and complex for even intermediate programmers. The mathematics behind the cute ML frameworks are scary. But once we understood a prerequisites of ML, then starting to code neural network from scratch is a good idea.

3. Steps

  • Create a FF layer class.
  • Create a NN class which will bind FF layers and also does training.

OOP is a very awesome feature of python and using the object of FF layer class, we can access its attributes and methods anywhere at any time.

3.1 Creating a FF layer class.

3.1.1 As usual, importing necessary requirements.

import numpy as np

3.1.2 Next, create a class and initialize it with possible parameters.

    def __init__(self, input_shape=None, neurons=1, bias=None, weights=None, activation=None, is_bias = True):
        self.input_shape = input_shape
        self.neurons = neurons
        self.isbias = is_bias = ""
        self.w = weights
        self.b = bias
        if input_shape != None:
            self.output_shape = neurons
        if self.input_shape != None:
            self.weights = weights if weights != None else np.random.randn(self.input_shape, neurons)
            self.parameters = self.input_shape *  self.neurons + self.neurons if self.isbias else 0  
            self.biases = bias if bias != None else np.random.randn(neurons)
            self.biases = 0  
        self.out = None
        self.input = None
        self.error = None = None
        activations = ["relu", "sigmoid", "tanh", "softmax"]
        self.delta_weights = 0
        self.delta_biases = 0
        self.pdelta_weights = 0
        self.pdelta_biases = 0        
        if activation not in activations and activation != None:
             raise ValueError(f"Activation function not recognised. Use one of {activations} instead.")
            self.activation = activation    
  • input_shape : It is for the number of input from the previous layer's neurons.
  • neurons : How many neurons are on this layer?
  • activation: What activation function to use?
  • bias: A bias value if is_bias is true.
  • isbias : Will we use bias? Inside __init__

  • To store the name of this layer.
  • self.weights: A connection strength or weights from previous to this layer. Use from np.random.randn(n_input, neurons) if not given.
  • self.biases : A bias value. On this layer.
  • self.out : Output of this layer.
  • self.input : Input to this layer. Is the input data for the input layer, and is output of the previous layer for all others.
  • self.error : Error term of this layer.
  • self.delta_weights : \begin{equation}\delta{w}\end{equation}
  • self.delta_biases : \begin{equation}\delta{b}\end{equation}
  • self.pdelta_weights : Previous self.delta_weights
  • self.pdelta_biases : Previous self.delta_biases
  • activations : A list of possible activation functions. If the given activation function is not recognised, raise an error.
  • self.activation : A variable to store activation function of this layer.

3.1.3 Now prepare the activation functions. For begining, we will use only few.

    def activation_fn(self, r):
        A method of FFL which contains the operation and definition of a given activation function.
        if self.activation == None or self.activation == "linear":
            return r  
        if self.activation == 'tanh': #tanh
            return np.tanh(r)
        if self.activation == 'sigmoid':  # sigmoid
            return 1 / (1 + np.exp(-r))
        if self.activation == "softmax":# stable softmax  
            r = r - np.max(r)
            s = np.exp(r)
            return s / np.sum(s)

Recall the mathematics,

\begin{equation} i. tanh(soma) = \frac{1-soma}{1+soma} \end{equation}

\begin{equation} ii. linear(soma) = soma \end{equation}

\begin{equation} iii. sigmoid(soma) = \frac{1}{1 + exp^{(-soma)}} \end{equation}

\begin{equation} iv. relu(soma) = \max(0, soma) \end{equation}

\begin{equation} v. softmax(x_j) = \frac{exp^{(x_j)}}{\sum_{i=1}^n{exp^{(x_i)}}} \end{equation}

\begin{equation} Where, soma = XW + \theta \end{equation}

And W is the weight vector of shape (n, w). X is input vector of shape (m, n) and πœƒ is bias term of shape w, 1.

def activation_dfn(self, r):
            A method of FFL to find the derivative of a given activation function.
        if self.activation is None:
            return np.ones(r.shape)
        if self.activation == 'tanh':
            return 1 - r ** 2
        if self.activation == 'sigmoid':
            return r * (1 - r)
        if self.activtion == 'softmax':
            soft = self.activation_fn(r)
            return soft * (1 - soft)
        if self.activation=='relu':
            return r

Let's revise a bit of calculus. Why do we need a derivative?

Well, if you are here then you already know that gradient descent is based upon the derivatives(gradients) of activation functions and errors. So we need to perform this derivative. But you are on your own to perform calculations. I will also explain the gradient descent later.

\begin{equation} i. \frac{d(linear(x))}{d(x)} = 1 \end{equation}

\begin{equation} ii. \frac{d(sigmoid(x))}{d(x)} = sigmoid(x)(1- sigmoid(x)) \end{equation}

\begin{equation} iii. \frac{d(tanh(x))}{d(x)} = 1-tanh(x)**2 \end{equation}

\begin{equation} iv. \frac{d(relu(x))}{d(x)} = 1 if x>0 else 0 \end{equation}

\begin{equation} v. \frac{d(softmax(x_j))}{d(x_k)} = softmax(x_j)(1- softmax(x_j)) \space when \space j = k \space else
\space -softmax({x_j}).softmax({x_k}) \end{equation}

For the sake of simplicity, we use the case of j = k for softmax.

3.1.4 Next create a method to perform activation.

    def apply_activation(self, x):
        soma =, self.weights) + self.biases
        self.out = self.activation_fn(soma)

This method takes the input vector x and performs the linear combination and then applies activation function to this value. The soma term is the total input to this node.

3.1.5 Next create a method to set the new weight vector.

This method is called when this layer is hidden. If a layer is hidden, we won't give input shape but only the neurons on this layer. So we must set the n_inputmanually and the same as weights. This method is used when we will be stacking the layers to make a <b>sequential</b> model.

    def set_n_input(self):
        self.weights = self.w if self.w != None else np.random.normal(size=(self.n_input, self.neurons))

I think we have made a simple Feedforward layer. Now is the time for us to create a class which can stack these layers together and also perform operations like train.

3.1.6 Next create a method to get total parameters of this layer:

    def get_parameters(self):
        self.parameters = self.input_shape *  self.neurons + self.neurons if self.isbias else 0  
        return self.parameters

Total parameters of a layer is a total number of weights plus total biases.

3.1.7 Now create a method which will call above get_parameters and set_n_input also do additional task and

    def set_output_shape(self):
        self.output_shape = self.neurons

This method will be called from the stacking class. And I have made this method to be identical to the CNN layers.

3.1.8 Finally, last but not least, a backpropagation method of this layer.

<b> Note that every layer has a different way of passing error backwards. I have done CNN from scratch hence I am making this article to support that one also.</b>

    def backpropagate(self, nx_layer):
        self.error =, = self.error * self.activation_dfn(self.out)
        self.delta_weights += * np.atleast_2d(self.input).T
        self.delta_biases +=

Here, nx_layer is the next layer. Let me share a little equation from <b>Tom M Mitchell's ML book(page 80+)</b>.

If the layer is output layer then its error is final error: \begin{equation} \delta_j = \frac{d(E_j)}{d(o_j)} f^1(o_j) \end{equation} And for all hidden and input layers: \begin{equation} \delta_j = - \frac{d(E_j)}{d(net_j)} = f^1(o_j) \sum_{k=downstream(j)} \delta_k w_{kj} \end{equation}

Note that: If this layer is the output layer, then the error will be the final error and we will not call this method. The term 𝑑(𝐸𝑗)/𝑑(π‘œπ‘—) is the derivative of error function wrt. output. I will share some explanations later on Gradient Descent.

Again going back to our method backpropagate here, this method is called only when this layer is not the final layer. Otherwise the next layer won't exist. Let's take a look into self.error, it is brought to this layer from its immediate layer or called downstream(j) here. Then we find the delta term. We need the first derivative of the activation function of this layer and we do it wrt output. When the term delta for this layer is found, we can get delta_weights for this layer by multiplying delta with this layer's most recent input. Similarly delta_biases is just the term delta. Note that, the len of delta will be equal to a total number of neurons. It stores the delta term for this layer.

3.2 Writing a stackking class

AHHHH long journey Aye!!

We will name it NN. And we will perform all training operations under this class.

3.2.1 Initializing a class.

(Note that:- the assumption of how many attributes we need will always fail, you might use less than initialized or you will create later on). Please follow the written comments below, for explanation.

    def __init__(self):
        self.layers = [] # a list to stack all the layers
        self.info_df = {} # this dictionary will store the information of our model
        self.column = ["LName", "Input", "Output", "Activation", "Bias"] # this list will be used the header of our summary
        self.parameters = 0 # how many parameters do we have?
        self.optimizer = "" # what optimizer are we using?
        self.loss = "" # what loss function are we using?
        self.all_loss = {} # loss through very epochs, needed for visualizing = 1 # learning rate
        self.metrics = []
        self.av_optimizers = ["sgd", "iterative", "momentum", "rmsprop", "adagrad", "adam", "adamax", "adadelta"] # available optimizers
        self.av_metrics = ["mse", "accuracy", "cse"] # available metrics
        self.av_loss = ["mse", "cse"] # available loss functions
        self.iscompiled = False # if model is compiled
        self.batch_size = 8 # batch size of input = 0.0001 # momentum rate, often called velocity
        self.all_acc = {} # all accuracy
        self.eps = 1e-8 # epsilion, often used to avoid divide by 0.

And hold on, we will write all optimizers from scratch too.

3.2.2 Writing a method for stackking layers.

  def add(self, layer):
        if(len(self.layers) > 0):
            prev_layer = self.layers[-1]
            if != "Input Layer":
       = f"Hidden Layer{len(self.layers) - 1}"
            if layer.input_shape == None:
                layer.input_shape = prev_layer.output_shape
   = "Output Layer"
            if prev_layer.neurons != layer.input_shape and layer.input_shape != None:
                raise ValueError(f"This layer '{}' must have neurons={prev_layer.neurons} because '{}' has output of {prev_layer.neurons}.")
   = "Input Layer"

Lots of dumb things happening under this method. It takes the object of the layer and stacks it to the previous layer. First we check if we have more than 0 layers from self.layers. If we do, then we set prev_layer to the last layer of all layers. And if the name of prev_layer is not "Input Layer" we will name all hidden layers as "Hidden Layer". And if this layer's number of input is none, we set it to the number of neurons of prev_layer. Because any hidden layer will have input as the output of the previous layer. And then we call the set_output_shape method for weight initialization, and other tasks. Note that the number of bias terms is equal to the number of neurons or nodes, hence we won't have to set them like this. But if this layer's input is given and it doesn't match the number of neurons of the previous layer is not equal then this is invalid assumption and we will throw an error.

Second, if we have 0 layers, then it is obviously an Input layer. We name it so.

Finally we make a stack of layers(not the data structure stack but a list) by appending them to a list of layers.

3.2.3 Lets write a method for a summary. And yes we will test it right now.

    def summary(self):
        lname = []
        linput = []
        lneurons = []
        lactivation = []
        lisbias = []
        for layer in self.layers:
            self.parameters += layer.parameters
        model_dict = {"Layer Name": lname, "Input": linput, "Neurons": lneurons, "Activation": lactivation, "Bias": lisbias}    
        model_df = pd.DataFrame(model_dict).set_index("Layer Name")
        print("Total Parameters: ", self.parameters)

I am taking help from the pandas library here and instead of writing tables like output, why not use the table? Nothing huge is happening here, but we created a different list for layer name, input shape, neurons, activation, bias and appended every layer's value on this. Then after we collected every value of the attribute from every layer, we created a dictionary with the right keys. Then BAAAAM! We created a dataframe and set the index to Layer Name.

Let's write a example:-

model = NN()
model.add(FFL(input_shape=28*28, 10, activation="softmax"))

If there are no errors, then let's proceed.

3.2.4 Train Method

Afterall, what use of all those fancy methods if you still not get train method?
But before that, let's create a method to check if our dataset meets the requirements of the model.

    def check_trainnable(self, X, Y):
        if self.iscompiled == False:
            raise ValueError("Model is not compiled.")
        if len(X) != len(Y):
            raise ValueError("Length of training input and label is not equal.")
        if X[0].shape[0] != self.layers[0].input_shape:
            layer = self.layers[0]
            raise ValueError(f"'{}' expects input of {layer.input_shape} while {X[0].shape[0]} is given.")
        if Y.shape[-1] != self.layers[-1].neurons:
            op_layer = self.layers[-1]
            raise ValueError(f"'{}' expects input of {op_layer.neurons} while {Y.shape[-1]} is given.")  

This method takes training input and labels, and if it is all good then we can walk proudly to the train method. We are checking if the model is compiled. Well model compilation is done by another method and will be presented here. Then there are other cases of error. Please see the statement inside ValueError for explanation.

Let's write a compiling method, shall we?
What this method should do is, prepare a optimizer, prepare a loss fxn, learning rate and so on.

    def compile_model(self, lr=0.01, mr = 0.001, opt = "sgd", loss = "mse", metrics=['mse']):
        if opt not in self.av_optimizers:
            raise ValueError(f"Optimizer is not understood, use one of {self.av_optimizers}.")      
        for m in metrics:
            if m not in self.av_metrics:
                raise ValueError(f"Metrics is not understood, use one of {self.av_metrics}.")      
        if loss not in self.av_loss:
            raise ValueError(f"Loss function is not understood, use one of {self.av_loss}.")      
        self.loss = loss = lr = mr
        self.metrics = metrics
        self.iscompiled = True
        self.optimizer = Optimizer(layers=self.layers, name=opt, learning_rate=lr, mr=mr)
        self.optimizer = self.optimizer.opt_dict[opt]

This method is under development but the important part here is the last two lines. Optimizer(layers=self.layers, name=opt, learning_rate=lr, mr=mr) is a class which encapsulates all our optimizers. When calling a class, it will initialize all our optimizer's necessary terms also. I will provide that code also but let's take a look at some glimpse.

class Optimizer:
    def __init__(self, layers, name=None, learning_rate = 0.01, mr=0.001): = name
        self.learning_rate = learning_rate = mr
        keys = ["sgd"]
        values = [self.sgd]
        self.opt_dict = {keys[i]:values[i] for i in range(len(keys))}
        if name != None and name in keys:
            self.opt_dict[name](layers=layers, training=False)
    def sgd(self, layers, learning_rate=0.01, beta=0.001, training=True):
        learning_rate = self.learning_rate
        for l in layers:
            if l.parameters !=0:
                if training:
                    l.weights += l.pdelta_weights* + l.delta_weights * learning_rate
                    l.biases += l.pdelta_biases* + l.delta_biases * learning_rate
                    l.pdelta_weights = l.delta_weights
                    l.pdelta_biases = l.delta_biases

We will be using only Gradient Descent here. I will also provide code to other optimizers on another blog. Things to note are, we create a key as a normal string of corresponding optimizer and value as a method. Gradient Descent

(Refer from the chapter 4 (page 80) of Machine Learning by <b> Tom M. Mitchell</b>.)

For weight update, we use this concept along with Back Propagation. Let's first prepare notations. \begin{equation} E_j\ is\ error\ function. \end{equation} \begin{equation} net_j\ is\ soma\ i.e. XW + \theta\ or\ \sum_i{w_{ji}x_{ji}} \end{equation} \begin{equation} o_j\ is\ the\ output\ of\ unit\ j\ due\ to\ the\ activation\ function\ i.e.\ o_j = f(net_j) \end{equation} \begin{equation} t_j\ is\ target\ for\ j \end{equation} \begin{equation} w_{ji}\ is\ weight\ value\ from\ j^{th}\ unit\ to\ i^{th}\ unit. \end{equation} \begin{equation} x_{ji} is\ the\ input\ value\ from\ j^{th}\ unit\ to\ i^{th}\ unit. \end{equation}

Note that 𝑑(𝐸𝑗)/𝑑(𝑀𝑗𝑖) varies with the case, if jth unit is output unit or internal.

  • Case 1: <b>j is output unit</b>. \begin{equation} \frac{d(E_j)}{d({w_{ji})}} = \frac{d(E_j)}{d({net_j})} \frac{d(net_j)}{d({w_{ji}})}
    \end{equation} \begin{equation} \space = \frac{d(E_j)}{d_{net_j}} x_{ji} \end{equation} \begin{equation} \ = \frac{d(E_j)}{d(o_j)} \frac{d(o_j)}{d(net_j)}x_{ji} \end{equation} \begin{equation} \ = \frac{d(E_j)}{d(o_j)} f^1(o_j) x_{ji} \end{equation}

  • Case 2: <b>j is hidden unit,</b>
    We have to refer to the set of all units immediately downstream of unit j.(i.e all units whose direct i/p include o/p of unit j) and denoted by downstream(j). And net_j can influence network o/p by only downstream(j).

\begin{equation} \frac{d(E_j)}{d({net_{j})}} = \sum_{k=downstream(j)} \frac{d(E)}{d({net_k})} \frac{d(net_k)}{d({net_{j}})} \end{equation} \begin{equation} \ = \sum_{k=downstream(j)} -\delta_k \frac{d(net_k)}{d({o_{j}})} \frac{d(o_j)}{d({net_{j}})} \end{equation} \begin{equation} \ = \sum_{k=downstream(j)} -\delta_k w_{kj} f^1(oj) \end{equation} \begin{equation} \ reordering\ terms, \end{equation} \begin{equation} \ \delta_j = - \frac{d(E_j)}{d(net_j)} = f^1(o_j) \sum_{k=downstream(j)} \delta_k w_{kj} \end{equation}

And the weight update term for all units is:- \begin{equation} \triangle w_{ji} = \alpha \delta_j x_{ji} \end{equation} \begin{equation} \ when\ momentum\ term\ is\ applied, \end{equation} \begin{equation} \triangle w_{ji}(n) = \beta \delta_j x_{ji} + \triangle w_{ji}(n-1) \end{equation} \begin{equation} \ \beta\ is\ momentum\ rate \end{equation} \begin{equation} \delta_j\ formula\ varies\ with\ the\ unit\ being\ output\ or\ internal. \end{equation} \begin{equation} w_{ji} = w_{ji} - \triangle w_{ji}\ \end{equation}

<b> The Gradient Descent algorithm will be easier to understand after we specify the activation function and loss function. Which I will be covering on below parts.</b>

3.2.5 Training Method

def train(self, X, Y, epochs, show_every=1, batch_size = 32, shuffle=True):
        self.check_trainnable(X, Y)
        self.batch_size = batch_size
        t1 = time.time()
        len_batch = int(len(X)/batch_size)
        batches = []
        curr_ind = np.arange(0, len(X), dtype=np.int32)
        if shuffle:
        if len(curr_ind) % batch_size != 0:
        batches = np.array_split(curr_ind, len_batch)
        for e in range(epochs):            
           err = []
            for batch in batches:
                curr_x, curr_y = X[batch], Y[batch]
                b = 0
                batch_loss = 0
                for x, y in zip(curr_x, curr_y):
                    out = self.feedforward(x)
                    loss, error = self.apply_loss(y, out)
                    batch_loss += loss
                    update = False
                    if b == batch_size-1:
                        update = True
                        loss = batch_loss/batch_size
                    self.backpropagate(loss, update)
            if e % show_every == 0:      
                out = self.feedforward(X)
                loss, error = self.apply_loss(Y, out)
                out_activation = self.layers[-1].activation
                if out_activation == "softmax":
                    pred = out.argmax(axis=1) == Y.argmax(axis=1)
                elif out_activation == "sigmoid":
                    pred = out > 0.7                    
                elif out_activation == None:
                    pred = abs(Y-out) < 0.000001                    
                self.all_loss[e] = round(error.mean(), 4)
                self.all_acc[e] = round(pred.mean() * 100, 4)                
                print(f"Time: {round(time.time() - t1, 3)}sec")
                t1 = time.time()
                print('Epoch: #%s, Loss: %f' % (e, round(error.mean(), 4)))
                print(f"Accuracy: {round(pred.mean() * 100, 4)}%")    

Alright folks, this is the train method. I hope you are not scared with the size. Some major steps:

  • Check if the dataset is trainable or not
  • Start a timer(or should we start timer after making batches)
  • Create a indices of dataset
  • If shuffle, then we do shuffle
  • Then we create indices for each batch, we also make each batch of mostly the same size but on odd cases np.array_split does work.
  • On every epoch:
    • For each batch:
      • For each x, y on batch:
        • Feed Forward the example set, (method is given below)
        • Find the loss for last layer and error, (method is given below)
        • Add loss to batch loss
        • If current example is last of batch, then we will update parameters
        • We backpropagate the error of current example, (the backpropagate method is given below)
    • If we want to show on this epoch,
      • Feedforward all trainsets and take training output.
      • Find train error
      • Find accuracy
      • Take the average of error and accuracy and show them.
      • Store loss and accuracy of this epoch(we will visualize later)

3.2.6 Write a feedforward method.

    def feedforward(self, x):
        for l in self.layers:
            l.input = x
            x = l.apply_activation(x)  
            l.out = x
        return x

Nothing strange is happening here. We take an input vector of a single example and pass it to the first layer. Then we set the input of that layer to x and get the output of this layer. And also set out of this layer to output given by the apply_activation method of that layer. Note that we need the output of this every layer for backpropagation and also the output of one layer acts as input to another. When there are no layers left, we pass the output of the last layer(o/p layer) as the output of this input.

3.2.7 Next we need a method to find error. We have few error functions on our assumption.

def apply_loss(self, y, out):
    if self.loss == "mse":
        loss = y - out
        mse = np.mean(np.square(loss))      
        return loss, mse
    if self.loss == 'cse':
        """ Requires out to be probability values. """    
        if len(out) == len(y) == 1: #print("Using Binary CSE.")            
            cse = -(y * np.log(out) + (1 - y) * np.log(1 - out))
            loss = -(y / out - (1 - y) / (1 - out))
        else: #print("Using Categorical CSE.")            
            if self.layers[-1].activation == "softmax":
                """if o/p layer's fxn is softmax then loss is y - out
                check the derivation of softmax and crossentropy with derivative"""
                loss = y - out
                loss = loss / self.layers[-1].activation_dfn(out)
                y = np.float64(y)
                out += self.eps
                loss = -(np.nan_to_num(y / out) - np.nan_to_num((1 - y) / (1 - out)))
            cse = -np.sum((y * np.nan_to_num(np.log(out)) + (1 - y) * np.nan_to_num(np.log(1 - out))))
        return loss, cse

The code is pretty weird but math is cute.

  • MSE(Mean Squared Error):- Mean of Squared Error. \begin{equation} E = \frac{1}{m} \sum_{i=1}^m(t_i - o_i)^2 \end{equation} where o is the output of the model and t is target or true label.

  • CSE(Cross Entropy):- Good for penalizing bad predictions more. \begin{equation} E = \frac{1}{m}\sum_{i=1}^{m} -y*log(h_{(\theta)}(x^i) - (1-y)*log(1-h_{(\theta)}(x^i) \end{equation} The loss value returned from the above equation is the term required for gradient descent. It will be clear by viewing Gradient Descent.

Recall the delta term from <b>Gradient Descent</b>, as the delta term depends upon the derivative of error function w.r.t weight, we need to find it. In fact our target is to find the term 𝑑(𝐸𝑗)/𝑑(π‘œπ‘—). It is not that hard by the way.
i. MSE \begin{equation} \frac{d(E_j)}{d(o_j)} = \frac{d\frac{1}{m} \sum_{i=1}^m(t_i - o_i)^2}{d(o_j)}\ \end{equation} \begin{equation} above\ term\ is\ 0\ for\ all\ except\ i=j\ \end{equation} \begin{equation} \therefore\ \frac{d(E_j)}{d(o_j)} = \frac{d\frac{1}{m} (t_j - o_j)^2}{d(o_j)}\ \end{equation} \begin{equation} \ = -(t_j - o_j)\ \end{equation} \begin{equation} \ and\ term\ \frac{d(E_j)}{d(net_j)} = -(t_j - o_j) f^1(o_j) \end{equation}

ii. CSE I am skipping long derivatives but note that d(log(x))/d(x) = 1/x. \begin{equation} E = \frac{1}{m}\sum_{i=1}^{m} -t_i*log(o_i) - (1-t_i)*log(1-o_i)\ \end{equation} \begin{equation} \ now\ term\ \frac{d(E_j)}{d(o_j)} = - \frac{t_i}{o_i} + \frac{1-t_i}{1-o_i} will\ be\ calculated. \end{equation}

Now going back to our code, what if we have an activation function softmax for the output layer? Well, since we will be using its derivative as softmax(1-softmax). Here softmax is o. So if we rearrange terms, 𝑑(𝐸𝑗)/𝑑(π‘œπ‘—) = (o-t)/(o(1-o)). Hence the term 𝑑(𝐸𝑗)/𝑑(𝑀𝑗𝑖) will be (o-t) when using softmax and cross-entropy.
np.nan_to_num will turn nan value to 0 that we got from log or 1/0.

3.2.8 Backpropagate method:

    def backpropagate(self, loss, update = True):  
        for i in reversed(range(len(self.layers))):
            layer = self.layers[i]
            if layer == self.layers[-1]:
                layer.error = loss
       = layer.error * layer.activation_dfn(layer.out)
                layer.delta_weights += * np.atleast_2d(layer.input).T
                layer.delta_biases +=
                nx_layer = self.layers[i+1]
            if update:
                layer.delta_weights /= self.batch_size
                layer.delta_biases /= self.batch_size
        if update:      

This method is called per example on every batch on every epoch. What happens is, when we pass the loss of model and update term, it runs over every layer and checks updates the delta term for all parameters. More simply:

  • For every layer from output to input:
    • If this layer is output layer, find delta term now
    • If this layer isn't the output layer, call the backpropagate method of that layer and send the next layer also. (I have already provided an individual backpropagate method for Feedforward layer.)
    • If we want to update the parameters now, then average the delta terms
  • If we are updating, then call the optimizer method, if we look back to the compile method, then we can see that self.optimizer is holding a reference to the method of Optimizer class. We pass the entire layers again here.
  • Now we have updated our parameters, we need to zero all the gradient terms. So we have another method, zerograd.
def zerograd(self):
    for l in self.layers:
        l.delta_biases = 0

It is pretty simple here. But once we are working with more than one type of layer, it will get messy.

    from keras.datasets import mnist
    (x_train, y_train), (x_test, y_test) = mnist.load_data()
    x = x_train.reshape(-1, 28 * 28)
    x = (x-x.mean(axis=1).reshape(-1, 1))/x.std(axis=1).reshape(-1, 1)
    y = pd.get_dummies(y_train).to_numpy()
    m = NN()
    m.add(FFL(784, 10, activation="softmax"))
    m.compile_model(lr=0.01, opt="sgd", loss="cse", mr= 0.001)
    m.train(x[:], y[:], epochs=100, batch_size=32)

This is a classification problem.

I am using keras just for getting a mnist dataset. We can get mnist data from the official website also. Then we normalize our data by subtracting mean and dividing with its corresponding standard deviation. Thanks to NumPy. Then we converted our data to one hot encoding using the pandas method, get_dummies and convert it to a NumPy array. We created an object of NN class and then added a Feed Forward layer of input shape 784 and neurons 10, we gave activation function as softmax. Since mnist dataset is 28X28 on each example, we made single image of shape 28*28. Softmax function is very useful for classification problems and usually used on last layers. Something like below happens but accuracy increases very slowly.\

Time: 19.278sec
Epoch: #20, Loss: 3208783.038700
Accuracy: 88.55%

We can make our dataset a one hot encoded vector using the below method also:\

def one_hot_encoding(lbl, classes):
    encoded = np.zeros((len(lbl), classes))
    c = list(set(lbl))
    if len(c) != classes:
        raise ValueError("Number of classes is not equal to unique labels.")
    for i in range(len(yy)):
        for j in range(len(c)):
            if c[j] == lbl[i]:
                encoded[i, j] = 1
    return encoded

With model like below accuracy was great

m = NN()
m.add(FFL(784, 100, activation="sigmoid"))
m.add(FFL(100, 10, activation="softmax"))
m.compile_model(lr=0.01, opt="adam", loss="cse", mr= 0.001)
m.train(x[:], y[:], epochs=100, batch_size=32)

4. Let's do something interesting.

4.1 Preparing Train/Validate data

Up to now, we have done some training only. But it is <b>not a good idea to boast the train accuracy.</b> We need to take validation data also. For that lets modify our few methods. First, we will edit __init__ method of our NN.\

self.train_loss = {} # to store train loss per view_every
self.val_loss = {} # to store val loss per view_every
self.train_acc = {} # to store train acc per view_every
self.val_acc = {} # to store val acc per view_every

Next, change train method as below:\

def train(self, X, Y, epochs, show_every=1, batch_size = 32, shuffle=True, val_split=0.1, val_x=None, val_y=None):    
        self.check_trainnable(X, Y)
        self.batch_size = batch_size
        t1 = time.time()
        curr_ind = np.arange(0, len(X), dtype=np.int32)
        if shuffle:
        if val_x != None and val_y != None:
            self.check_trainnable(val_x, val_y)
            print("\nValidation data found.\n")
            val_ex = int(len(X) * val_split)
            val_exs = []
            while len(val_exs) != val_ex:
                rand_ind = np.random.randint(0, len(X))
                if rand_ind not in val_exs:
            val_ex = np.array(val_exs)
            val_x, val_y = X[val_ex], Y[val_ex]
            curr_ind = np.array([v for v in curr_ind if v not in val_ex])                
        print(f"\nTotal {len(X)} samples.\nTraining samples: {len(curr_ind)} Validation samples: {len(val_x)}.")          
        batches = []
        len_batch = int(len(curr_ind)/batch_size)
        if len(curr_ind)%batch_size != 0:
        batches = np.array_split(curr_ind, len_batch)    
        print(f"Total {len_batch} batches, most batch has {batch_size} samples.\n")      
        batches = []
        if(len(curr_ind) % batch_size) != 0 :
            nx = batch_size-len(curr_ind) % batch_size
            nx = curr_ind[:nx]
            curr_ind = np.hstack([curr_ind, nx])  
        batches = np.split(curr_ind, batch_size)  
        for e in range(epochs):            
            err = []
            for batch in batches:
                a = []
                curr_x, curr_y = X[batch], Y[batch]
                b = 0
                batch_loss = 0
                for x, y in zip(curr_x, curr_y):
                    out = self.feedforward(x)
                    loss, error = self.apply_loss(y, out)
                    batch_loss += loss
                    update = False
                    if b == batch_size-1:
                        update = True
                        loss = batch_loss/batch_size
                    self.backpropagate(loss, update)
            if e % show_every == 0:      
                train_out = self.feedforward(X[curr_ind])
                train_loss, train_error = self.apply_loss(Y[curr_ind], train_out)
                out_activation = self.layers[-1].activation
                val_out = self.feedforward(val_x)
                val_loss, val_error = self.apply_loss(val_y, val_out)
                if out_activation == "softmax":
                    train_acc = train_out.argmax(axis=1) == Y[curr_ind].argmax(axis=1)
                    val_acc = val_out.argmax(axis=1) == val_y.argmax(axis=1)
                elif out_activation == "sigmoid":
                    train_acc = train_out > 0.7
                    val_acc = val_out > 0.7
                elif out_activation == None:
                    train_acc = abs(Y[curr_ind]-train_out) < 0.000001
                    val_acc = abs(Y[val_ex]-val_out) < 0.000001                    
                self.train_loss[e] = round(train_error.mean(), 4)
                self.train_acc[e] = round(train_acc.mean() * 100, 4)                
                self.val_loss[e] = round(val_error.mean(), 4)
                self.val_acc[e] = round(val_acc.mean()*100, 4)
                print(f"Epoch: {e}, Time: {round(time.time() - t1, 3)}sec")              
                print(f"Train Loss: {round(train_error.mean(), 4)} Train Accuracy: {round(train_acc.mean() * 100, 4)}%")
                print(f'Val Loss: {(round(val_error.mean(), 4))} Val Accuracy: {round(val_acc.mean() * 100, 4)}% \n')
                t1 = time.time()

The pseudo code or explanation of above code is:

  • Check trainable training data.
  • Prepare indices from 0 to no. examples.
  • If validation data is given on val_x, val_y then check their trainability also.
  • Else, we will split the prepared indices of data for train and validation.
  • First we get a number of indices for validation, then get indices for them and data too.
  • We will also edit curr_ind Instead of using actual data, I am using only indices because of memory.
  • Then train just as above processes.
  • For show_every, We do pass entire train data and get accuracy, loss. And do a similar validation set.

4.2 Lets add some visualizing methods

    def visualize(self):
        k = list(self.train_loss.keys())
        v = list(self.train_loss.values())
        plt.plot(k, v, "g-")
        k = list(self.val_loss.keys())
        v = list(self.val_loss.values())
        plt.plot(k, v, "r-")
        plt.legend(["Train Loss", "Val Loss"])
        plt.title("Loss vs Epoch")
        k = list(self.train_acc.keys())
        v = list(self.train_acc.values())
        plt.plot(k, v, "g-")
        k = list(self.val_acc.keys())
        v = list(self.val_acc.values())
        plt.plot(k, v, "r-")
        plt.title("Acc vs epoch")
        plt.legend(["Train Acc", "Val Acc"])

Nothing strange is happening here. We are only using the keys and values of previously stored train/val acc/loss. If we set show_every=1 then, the graph will be shown great.

5 Finally

My version of the final Feedforward Deep Neural Network will be given on the link and in the meantime, I am gonna share my results.

    from keras.datasets import mnist
    (x_train, y_train), (x_test, y_test) = mnist.load_data()
    x = x_train.reshape(-1, 28 * 28)
    x = (x-x.mean(axis=1).reshape(-1, 1))/x.std(axis=1).reshape(-1, 1)
    y = pd.get_dummies(y_train).to_numpy()
    xt = x_test.reshape(-1, 28 * 28)
    xt = (xt-xt.mean(axis=1).reshape(-1, 1))/xt.std(axis=1).reshape(-1, 1)
    yt = pd.get_dummies(y_test).to_numpy()
    m = NN()
    m.add(FFL(784, 10, activation='sigmoid'))
    m.add(FFL(10, 10, activation="softmax"))
    m.compile_model(lr=0.01, opt="adam", loss="cse", mr= 0.001)
    m.train(x[:], y[:], epochs=10, batch_size=32, val_x=xt, val_y = yt)

6 Bonus Topics

6.1 Saving Model on JSON File

import os
import json
def save_model(self, path="model.json"):
        path:- where to save a model including filename
        saves Json file on given path.
    dict_model = {"model":str(type(self).__name__)}
    to_save = ["name", "isbias", "neurons", "input_shape", "output_shape", "weights", "biases", "activation", "parameters"]
    for l in self.layers:
        current_layer = vars(l)
        values = {"type":str(type(l).__name__)}
        for key, value in current_layer.items():
            if key in to_save:
                if key in ["weights", "biases"]:
                    value = value.tolist()
                values[key] = value
        dict_model[] = values
    json_dict = json.dumps(dict_model)    
    with open(path, mode="w") as f:

Note that, we are not saving parameters on encrypted form and neither are we saving it on different files.

  • We want to save everything in JSON format, so we are creating a dictionary first.
  • vars(obj) allows us to create a dictionary from the attrib:value structure of the class object.
  • We are about to save only a few things necessary to use a model. to_save is a list of all the attributes that we need to predict a model.
  • Still we haven't implemented a way to check if the saved model is compiled or not. But we do need a predict method.

6.2 Loading a JSON Model

def load_model(path="model.json"):
        path:- path of model file including filename
        returns:- a model
    models = {"NN": NN}
    layers = {"FFL": FFL}
    """layers = {"FFL": FFL, "Conv2d":Conv2d, "Dropout":Dropout, "Flatten": Flatten, "Pool2d":Pool2d}"""
    with open(path, "r") as f:
        dict_model = json.load(f)
        model = dict_model["model"]
        model = models[model]()
        for layer, params in dict_model.items():
            if layer != "model":                
                lyr = layers[params["type"]](neurons=params["neurons"])# create a layer obj
                if params.get("weights"):
                    lyr.weights = params["weights"]
                if params.get("biases"):
                    lyr.biases = params["biases"]
       = layer
                lyr.activation = params["activation"]
                lyr.isbias = params["isbias"]
                lyr.input_shape = params["input_shape"]
                lyr.output_shape = params["output_shape"]
                lyr.neurons = params["neurons"]
                lyr.parameters = params["parameters"]
        return model
m = load_model()
  • Nothing is strange here. But a few things to note is, FFL is a method's address. And NN is a class which we will call later.
  • The model is created on line model = models[model]().
  • First test of if our model works or not can be seen from m.summary().
  • Next try to use the predict(x) method.

6.3 Predict Method

    def predict(self, X):
        out = []
        for x in X:
        return out

Now, this is where this blog ends but I have written another blog, Convolutional Neural Network from Scratch too. I hope you’ve found this blog to be useful and this will be helpful when you try to write your own version of a neural network from scratch.

7 References and Credits

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