Close Icon
Article AI Blog CPG General Healthcare High Tech Insurance Life Sciences November 1, 2017 6 minute read

Deep Learning Diaries: Building Custom Layers in Keras

There are many deep learning libraries available, some are more popular than the others, and some get used for very specific tasks.  Abhai Kollara discusses the merits of Keras and walks us through various examples of its uses and functionalities. He also compares it with some of the popular libraries.

Natural Language Processing or Computer Vision are some of the hardest problems in Artificial Intelligence. In the past couple of years, a lot of those problems are solved to near, or better than, human accuracy using Deep Learning.

Deep Learning community is quite open; they share lot of information. Many open source contributors are working towards making Deep Learning packages quite useful and stable. I am proud to have contributed to Keras Deep Learning Package. Keras is a popular Deep Learning package that has made the process of solving Deep Learning problems similar to building Lego blocks.

Keras is currently one of the most commonly used deep learning libraries today. Part of the reason why it’s so popular is its API. Keras was built as a high-level API for other deep learning libraries, which means Keras does not perform low-level tensor operations, instead it provides an interface to its backend which is built for such operations. This allows Keras to abstract a lot of the underlying details and allows the programmer to concentrate on the architecture of the model. Currently Keras supports TensorFlow, Theano, and CNTK as its backend.

Let’s explore this further. TensorFlow is a backend used by Keras. Here’s the code for MNIST classification in TensorFlow and Keras. Both models are nearly identical and applies to the same problem. But if you compare the codes, you get an idea of the abstraction Keras provides you. The entire model is defined within 10 lines of code!

model = Sequential()

model.add(Conv2D(32, kernel_size=(3, 3), activation='relu', input_shape=input_shape))

model.add(Conv2D(64, (3, 3), activation='relu'))

model.add(MaxPooling2D(pool_size=(2, 2)))



model.add(Dense(128, activation='relu'))


model.add(Dense(num_classes, activation='softmax'))

You can visit the official documentation for understanding the basic usage of Keras.

Sequential API vs Functional API

Keras has two API models – Sequential and Functional.

The sequential model is helpful when your model is simply one layer after the other. You can use model.add() to stack layers and model.compile to compile the model with required loss function and optimizers. The example at the beginning uses the sequential model. As you can see, the sequential model is simple to use.

The functional API brings out the real power of Keras. If you want to build complex models with multiple inputs or models with shared layers, functional API is the way to go. Let’s see an example:

from keras.layers import Input, Dense

from keras.models import Model

# This returns a tensor

inputs = Input(shape=(784,))

# a layer instance is callable on a tensor, and returns a tensor

x = Dense(64, activation=’relu’)(inputs)

x = Dense(64, activation=’relu’)(x)

predictions = Dense(10, activation=’softmax’)(x)

# This creates a model that includes

# the Input layer and three Dense layers

model = Model(inputs=inputs, outputs=predictions)



metrics=[‘accuracy’]), labels) # starts training

Here, the layers take a more functional form as compared to the sequential model. The inputs to each layer are explicitly specified and you have access to the output of each layer. This allows you to share the tensors with multiple layers. The functional API also gives you control over the model inputs and outputs as seen above.

Keras Computational Graph

Before we write our custom layers, let’s take a closer look at the internals of Keras computational graph. Keras has its own graph that is different from that of its underlying backend. The Keras topology has 3 key classes that are worth understanding:

  • Layer encapsulates the weights and the associated computations of the layer. The call method of a layer class contains the layer’s logic. The layer has inbound_nodes and outbound_nodes attributes. Each time a layer is connected to a new input, a node is added to inbound_nodes. Each time the output of a layer is used by another layer, a node is added to outbound_nodes. The layer also carries a list of trainable and non-trainable weights of the layer.
  • Node represents the connection between two layers. node.outbound_layer points to the layer that converts the input tensor into output tensor. node.inbound_layers is a list of layers from where the input tensors originate. The node object carries other information like input and output shapes, masks, etc. along with the actual input tensors and output tensors.
  • Container is a directed acyclic graph of layers connected using nodes. It represents the topology of the model. This graph ensures the correct propagation of gradients to the inputs. The actual model couples the optimizer and training routines along with this.

Custom layers

Despite the wide variety of layers provided by Keras, it is sometimes useful to create your own layers, like when you are trying to implement a new layer architecture or create a layer that does not exist in Keras. Custom layers allow you to set up your own transformations and weights for a layer. Remember that if you do not need new weights and require stateless transformations, you can use the Lambda layer.

Now let’s see how we can define our custom layers. In Keras 2.0, there are three functions that needs to be defined for a layer:

  • build(input_shape)
  • call(input)
  • compute_output_shape(input_shape)

The build method is called when the model containing the layer is built. This is where you set up the weights of the layer. The input_shape is accepted as an argument to the function.

The call method defines the computations performed on the input. The function accepts the input tensor as its argument and returns the output tensor after applying the required operations.

Finally, we need to define the compute_output_shape function, which is required for Keras to infer the shape of the output. This allows Keras to do shape inference without actually executing the computation. The input_shape is passed as the argument.


Now let’s build our custom layer. For the sake of simplicity, we will be building a vanilla fully-connected layer (called Dense in Keras). First let’s make the required imports:

from keras import backend as K

from keras.engine.topology

import Layer

Now let’s create our layer named MyDense. Our new layer must inherit from the base Layer class. Set up __init__function to accept the number of units (accepted as output_dim) in the fully connected layer.

class MyDense(Layer):

def __init__(self, output_dim, **kwargs):

self.units = output_dim

super(MyLayer, self).__init__(**kwargs)

The build function is where we define the weights of the layer. The weights can be instantiated using the add_weightmethod of the layer class.

The name and shape arguments determine the name used for the backend variable and the shape of the weight variable respectively. If your input is of the shape (batch_size, input_dim), your weights need to be of the shape (input_dim, output_dim). Here, output dimension denotes the number of units in the layer.

Conversely, you may also specify an initializerregularizer and a constraint. The trainable argument can be set to False to prevent the weight from contributing to the gradient. Make sure you also call the build method of the base layer class.

def build(self, input_shape):

self.kernel = self.add_weight(name='kernel',

shape=(input_shape[1], self.output_dim),



super(MyLayer, self).build(input_shape)

The call function houses the logic of the layer. For our fully connected layer, it means that we have to calculate the dot product between the weights and the input. The input is passed as a parameter and the result of the dot product is returned.

def call(self, x):

y =, self.kernel)

return y

The compute_output_shape is a helper function to specify the change in shape of the input when it passes through the layer. Here our output shape will be (batch_size, output_dim):

def compute_output_shape(self, input_shape):

return (input_shape[0], self.output_dim)

That’s it, you’re good to go. You can use MyDense layer just like any other layer in Keras.

Keras vs Other DL Frameworks

I have seen a lot of discussions comparing deep learning frameworks that include Keras and personally, I think Keras should not be on the list. As I mentioned earlier, Keras is technically not a deep learning framework, it’s an API. It runs on top of other DL frameworks. The power of Keras is in its abstraction, while still giving you sufficient control over your architecture.

In case you decide that you need to play with lower level tensor operations, you can always go for other frameworks. TensorFlow seems to be the most popular these days. Backed by Google, it even has C++ and Go APIs. Theano was one of the first DL frameworks, but has been discontinued recently. PyTorch is an interesting competitor as well with its dynamic graphs. Unlike TensorFlow or Theano, which has static graphs, the computational graphs in PyTorch are built dynamically for each input. It is becoming increasingly popular amongst researchers due to its flexibility.

If you ask me, Keras is sufficient for most purposes. Even when you experiment with new architectures, the functional API combined with the access to backend functions, can get the job done. But that’s just me, a lot of people opt to directly go for TensorFlow and other libraries, so the choice is yours.

Saama can put you on the fast track to clinical trial process innovation.