Breast Cancer Detection Using CNN

Published by pasqualebrownlow on 5 September 20205 September 2020

Breast Cancer Detection Using CNN in Python

Breast cancer is the most commonly occurring cancer in women and the second most common cancer overall. There were over 2 million new cases in 2018, making it a significant health problem in present days.

The key challenge in breast cancer detection is to classify tumors as malignant or benign. Malignant refers to cancer cells that can invade and kill nearby tissue and spread to other parts of your body. Unlike cancerous tumor(malignant), Benign does not spread to other parts of the body and is safe somehow. Deep neural network techniques can be used to improve the accuracy of early diagnosis significantly.

Deep Learning is a subfield of machine learning concerned with algorithms inspired by the structure and function of the brain called an artificial neural network.

A Convolutional Neural Network (ConvNet/CNN) is a Deep Learning algorithm which can take in an input image, assign importance (learnable weights and biases) to various aspects/objects in the image and be able to differentiate one from the other. The pre-processing required in a ConvNet is much lower as compared to other classification algorithms.

What is Dropout

Dropout is a technique where randomly selected neurons are ignored during training. They are “dropped-out” randomly. This means that their contribution to the activation of downstream neurons is temporally removed on the forward pass and any weight updates are not applied to the neuron on the backward pass.

What is Batch Normalization

It is a technique which is designed to automatically standardize the inputs to a layer in a deep learning neural network.
e.g. We have four features having different unit after applying batch normalization it comes in similar unit.
By Normalizing the output of neurons the activation function will only receive inputs close to zero.
Batch normalization ensures a non vanishing gradient.

We are going to use tensorflow 2.3 to build the model. You can install tensorflow by running this command.

!pip install tensorflow-gpu==2.3.0-rc0

Importing necessary library that will use in model building.

import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import Sequential
from tensorflow.keras.layers import Flatten, Dense, Dropout, BatchNormalization
from tensorflow.keras.layers import Conv1D, MaxPool1D

from tensorflow.keras.optimizers import Adam


print(tf.__version__)

2.3.0

pandas for loading and manipulating the data.

NumPy is used for working with arrays. It also has functions for working in domain of linear algebra, fourier transform and matrices.

pyplot from matplotlib is used to visualize the results.

Seaborn is a Python data visualization library based on matplotlib. It provides a high-level interface for drawing attractive and informative statistical graphics.

import pandas as pd
import numpy as np
import  seaborn as sns
import matplotlib.pyplot as plt

/usr/local/lib/python3.6/dist-packages/statsmodels/tools/_testing.py:19: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
  import pandas.util.testing as tm

from sklearn import datasets, metrics
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler

Load and return the breast cancer classification dataset. The breast cancer dataset is a classic and very easy binary classification dataset.

cancer = datasets.load_breast_cancer()

We can view any particular column with the help of cancer.DESCR.

print(cancer.DESCR)

.. _breast_cancer_dataset:

Breast cancer wisconsin (diagnostic) dataset
--------------------------------------------

**Data Set Characteristics:**

    :Number of Instances: 569

    :Number of Attributes: 30 numeric, predictive attributes and the class

    :Attribute Information:
        - radius (mean of distances from center to points on the perimeter)
        - texture (standard deviation of gray-scale values)
        - perimeter
        - area
        - smoothness (local variation in radius lengths)
        - compactness (perimeter^2 / area - 1.0)
        - concavity (severity of concave portions of the contour)
        - concave points (number of concave portions of the contour)
        - symmetry 
        - fractal dimension ("coastline approximation" - 1)

        The mean, standard error, and "worst" or largest (mean of the three
        largest values) of these features were computed for each image,
        resulting in 30 features.  For instance, field 3 is Mean Radius, field
        13 is Radius SE, field 23 is Worst Radius.

        - class:
                - WDBC-Malignant
                - WDBC-Benign

    :Summary Statistics:

    ===================================== ====== ======
                                           Min    Max
    ===================================== ====== ======
    radius (mean):                        6.981  28.11
    texture (mean):                       9.71   39.28
    perimeter (mean):                     43.79  188.5
    area (mean):                          143.5  2501.0
    smoothness (mean):                    0.053  0.163
    compactness (mean):                   0.019  0.345
    concavity (mean):                     0.0    0.427
    concave points (mean):                0.0    0.201
    symmetry (mean):                      0.106  0.304
    fractal dimension (mean):             0.05   0.097
    radius (standard error):              0.112  2.873
    texture (standard error):             0.36   4.885
    perimeter (standard error):           0.757  21.98
    area (standard error):                6.802  542.2
    smoothness (standard error):          0.002  0.031
    compactness (standard error):         0.002  0.135
    concavity (standard error):           0.0    0.396
    concave points (standard error):      0.0    0.053
    symmetry (standard error):            0.008  0.079
    fractal dimension (standard error):   0.001  0.03
    radius (worst):                       7.93   36.04
    texture (worst):                      12.02  49.54
    perimeter (worst):                    50.41  251.2
    area (worst):                         185.2  4254.0
    smoothness (worst):                   0.071  0.223
    compactness (worst):                  0.027  1.058
    concavity (worst):                    0.0    1.252
    concave points (worst):               0.0    0.291
    symmetry (worst):                     0.156  0.664
    fractal dimension (worst):            0.055  0.208
    ===================================== ====== ======

    :Missing Attribute Values: None

    :Class Distribution: 212 - Malignant, 357 - Benign

We will be using pandas DataFrame to present all our data. We will create a dataframe with our cancer data and target data. It would help us to store all the inputs and outputs in one dataframe.

X = pd.DataFrame(data = cancer.data, columns=cancer.feature_names)
X.head()

	mean radius	mean texture	mean perimeter	mean area	mean smoothness	mean compactness	mean concavity	mean concave points	mean symmetry	mean fractal dimension	radius error	texture error	perimeter error	area error	smoothness error	compactness error	concavity error	concave points error	symmetry error	fractal dimension error	worst radius	worst texture	worst perimeter	worst area	worst smoothness	worst compactness	worst concavity	worst concave points	worst symmetry	worst fractal dimension
0	17.99	10.38	122.80	1001.0	0.11840	0.27760	0.3001	0.14710	0.2419	0.07871	1.0950	0.9053	8.589	153.40	0.006399	0.04904	0.05373	0.01587	0.03003	0.006193	25.38	17.33	184.60	2019.0	0.1622	0.6656	0.7119	0.2654	0.4601	0.11890
1	20.57	17.77	132.90	1326.0	0.08474	0.07864	0.0869	0.07017	0.1812	0.05667	0.5435	0.7339	3.398	74.08	0.005225	0.01308	0.01860	0.01340	0.01389	0.003532	24.99	23.41	158.80	1956.0	0.1238	0.1866	0.2416	0.1860	0.2750	0.08902
2	19.69	21.25	130.00	1203.0	0.10960	0.15990	0.1974	0.12790	0.2069	0.05999	0.7456	0.7869	4.585	94.03	0.006150	0.04006	0.03832	0.02058	0.02250	0.004571	23.57	25.53	152.50	1709.0	0.1444	0.4245	0.4504	0.2430	0.3613	0.08758
3	11.42	20.38	77.58	386.1	0.14250	0.28390	0.2414	0.10520	0.2597	0.09744	0.4956	1.1560	3.445	27.23	0.009110	0.07458	0.05661	0.01867	0.05963	0.009208	14.91	26.50	98.87	567.7	0.2098	0.8663	0.6869	0.2575	0.6638	0.17300
4	20.29	14.34	135.10	1297.0	0.10030	0.13280	0.1980	0.10430	0.1809	0.05883	0.7572	0.7813	5.438	94.44	0.011490	0.02461	0.05688	0.01885	0.01756	0.005115	22.54	16.67	152.20	1575.0	0.1374	0.2050	0.4000	0.1625	0.2364	0.07678

y = cancer.target

array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
       0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0...])

cancer.target_names

array(['malignant', 'benign'], dtype='<U9')

X.shape

(569, 30)

It is not possible for us to manually split our dataset also we need to split the dataset in a random manner. To help us with this task, we will be using a SciKit library named train_test_split. We will be using 80% of our dataset for training purposes and 20% for testing.

X_train, X_test, y_train, y_test = train_test_split(X, y, test_size = 0.2, random_state = 0, stratify = y)

X_train.shape

(455, 30)

X_test.shape

(114, 30)

StandardScaler removes the mean and scales the data to unit variance.

scaler = StandardScaler()
X_train = scaler.fit_transform(X_train)
X_test = scaler.transform(X_test)

X_train = X_train.reshape(455,30,1)
X_test = X_test.reshape(114, 30, 1)

Now, Let's go ahead and build our CNN model

A Sequential() function is the easiest way to build a model in Keras. It allows you to build a model layer by layer. Each layer has weights that correspond to the layer the follows it. We use the add() function to add layers to our model.

Conv1D() is a 1D Convolution Layer, this layer is very effective for deriving features from a fixed-length segment of the overall dataset, where it is not so important where the feature is located in the segment. In the first Conv1D() layer, we are learning a total of 36 filters with size of the convolutional window as 3. The input_shape specifies the shape of the input. It is a necessary parameter for the first layer in any neural network. We will be using the ReLu activation function. The rectified linear activation function or ReLU for short is a piecewise linear function that will output the input directly if it is positive, otherwise, it will output zero.

The Rectified Linear Unit(ReLu) is the most commonly used activation function in deep learning models. The function returns 0 if it receives any negative input, but for any positive value x it returns that value back. So it can be written as f(x)=max(0,x)

To stop problem of shrinkage of data we use concept called Padding.

It has two types:

valid
same

Flattening is converting the data into a 1-dimensional array for inputting it to the next layer. We flatten the output of the convolutional layers to create a single long feature vector.

The Sigmoid function takes a value as input and outputs another value between 0 and 1. It is non-linear and easy to work with when constructing a neural network model. The good part about this function is that continuously differentiable over different values of z and has a fixed output range.

epochs = 50
model = Sequential()
model.add(Conv1D(filters=32, kernel_size=2, activation='relu', input_shape = (30,1)))
model.add(BatchNormalization())
model.add(Dropout(0.2))

model.add(Conv1D(filters=64, kernel_size=2, activation='relu'))
model.add(BatchNormalization())
model.add(Dropout(0.5))

model.add(Flatten())
model.add(Dense(64, activation='relu'))
model.add(Dropout(0.5))

model.add(Dense(1, activation='sigmoid'))

model.summary()

Model: "sequential"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
conv1d (Conv1D)              (None, 29, 32)            96        
_________________________________________________________________
batch_normalization (BatchNo (None, 29, 32)            128       
_________________________________________________________________
dropout (Dropout)            (None, 29, 32)            0         
_________________________________________________________________
conv1d_1 (Conv1D)            (None, 28, 64)            4160      
_________________________________________________________________
batch_normalization_1 (Batch (None, 28, 64)            256       
_________________________________________________________________
dropout_1 (Dropout)          (None, 28, 64)            0         
_________________________________________________________________
flatten (Flatten)            (None, 1792)              0         
_________________________________________________________________
dense (Dense)                (None, 64)                114752    
_________________________________________________________________
dropout_2 (Dropout)          (None, 64)                0         
_________________________________________________________________
dense_1 (Dense)              (None, 1)                 65        
=================================================================
Total params: 119,457
Trainable params: 119,265
Non-trainable params: 192
_________________________________________________________________

Compile defines the loss function, the optimizer, and the metrics. That's all. It has nothing to do with the weights and you can compile a model as many times as you want without causing any problem to pretrained weights.

model.compile(optimizer=Adam(lr=0.00005), loss = 'binary_crossentropy', metrics=['accuracy'])

Trains the model for a fixed number of epochs (iterations on a dataset).

history = model.fit(X_train, y_train, epochs=epochs, validation_data=(X_test, y_test), verbose=1)

...
Epoch 46/50
15/15 [==============================] - 0s 6ms/step - loss: 0.1054 - accuracy: 0.9560 - val_loss: 0.1064 - val_accuracy: 0.9649
Epoch 47/50
15/15 [==============================] - 0s 6ms/step - loss: 0.1373 - accuracy: 0.9473 - val_loss: 0.1074 - val_accuracy: 0.9649
Epoch 48/50
15/15 [==============================] - 0s 7ms/step - loss: 0.1078 - accuracy: 0.9538 - val_loss: 0.1068 - val_accuracy: 0.9649
Epoch 49/50
15/15 [==============================] - 0s 6ms/step - loss: 0.0896 - accuracy: 0.9648 - val_loss: 0.1060 - val_accuracy: 0.9649
Epoch 50/50
15/15 [==============================] - 0s 6ms/step - loss: 0.0927 - accuracy: 0.9648 - val_loss: 0.1047 - val_accuracy: 0.9649

def plot_learningCurve(history, epoch):
  # Plot training & validation accuracy values
  epoch_range = range(1, epoch+1)
  plt.plot(epoch_range, history.history['accuracy'])
  plt.plot(epoch_range, history.history['val_accuracy'])
  plt.title('Model accuracy')
  plt.ylabel('Accuracy')
  plt.xlabel('Epoch')
  plt.legend(['Train', 'Val'], loc='upper left')
  plt.show()

  # Plot training & validation loss values
  plt.plot(epoch_range, history.history['loss'])
  plt.plot(epoch_range, history.history['val_loss'])
  plt.title('Model loss')
  plt.ylabel('Loss')
  plt.xlabel('Epoch')
  plt.legend(['Train', 'Val'], loc='upper left')
  plt.show()

A history object that contains all information collected during training.

history.history

{'accuracy': [0.6197802424430847,
  0.7494505643844604,
  0.795604407787323,
  0.8461538553237915,
  0.8395604491233826,
  0.8593406677246094,
  0.8901098966598511,
  0.8791208863258362,
  0.8813186883926392,
  0.9098901152610779,
  0.903296709060669,
  0.9230769276618958,
  ...]}

plot_learningCurve(history, epochs)

In Model accuracy graph A validation accuracy is always greater than train accuracy thats means our model is not overfitting.

In Model accuracy graph A validation loss is also very lower than training loss so unless and until validation loss goes above than the training loss than we can keep training our model.

We have successfully created our program to detect breast cancer using Deep neural network. We are able to classify cancer effectively with our CNN technique.

Breast Cancer Detection Using CNN