Heart Disease Prediction using Neural Networks¶
This project will focus on predicting heart disease using neural networks. Based on attributes such as blood pressure, cholestoral levels, heart rate, and other characteristic attributes, patients will be classified according to varying degrees of coronary artery disease. This project will utilize a dataset of 303 patients and distributed by the UCI Machine Learning Repository.
Machine learning and artificial intelligence is going to have a dramatic impact on the health field; as a result, familiarizing yourself with the data processing techniques appropriate for numerical health data and the most widely used algorithms for classification tasks is an incredibly valuable use of your time! In this tutorial, we will do exactly that.
We will be using some common Python libraries, such as pandas, numpy, and matplotlib. Furthermore, for the machine learning side of this project, we will be using sklearn and keras. Import these libraries using the cell below to ensure you have them correctly installed.
import sys
import pandas as pd
import numpy as np
import sklearn
import matplotlib
import keras
import matplotlib.pyplot as plt
from pandas.plotting import scatter_matrix
1. Importing the Dataset¶
The dataset is available through the University of California, Irvine Machine learning repository. Here is the URL:
http:////archive.ics.uci.edu/ml/datasets/Heart+Disease
This dataset contains patient data concerning heart disease diagnosis that was collected at several locations around the world. There are 76 attributes, including age, sex, resting blood pressure, cholestoral levels, echocardiogram data, exercise habits, and many others. To data, all published studies using this data focus on a subset of 14 attributes - so we will do the same. More specifically, we will use the data collected at the Cleveland Clinic Foundation.
To import the necessary data, we will use pandas' built in read_csv() function.
# import the heart disease dataset
url = "http://archive.ics.uci.edu/ml/machine-learning-databases/heart-disease/processed.cleveland.data"
# the names will be the names of each column in our pandas DataFrame
names = ['age',
'sex',
'cp',
'trestbps',
'chol',
'fbs',
'restecg',
'thalach',
'exang',
'oldpeak',
'slope',
'ca',
'thal',
'class']
# read the csv
cleveland = pd.read_csv(url, names=names)
# print the shape of the DataFrame, so we can see how many examples we have
print 'Shape of DataFrame: {}'.format(cleveland.shape)
print cleveland.loc[1]
# print the last twenty or so data points
cleveland.loc[280:]
# remove missing data (indicated with a "?")
data = cleveland[~cleveland.isin(['?'])]
data.loc[280:]
# drop rows with NaN values from DataFrame
data = data.dropna(axis=0)
data.loc[280:]
# print the shape and data type of the dataframe
print data.shape
print data.dtypes
# transform data to numeric to enable further analysis
data = data.apply(pd.to_numeric)
data.dtypes
# print data characteristics, usings pandas built-in describe() function
data.describe()
# plot histograms for each variable
data.hist(figsize = (12, 12))
plt.show()
2. Create Training and Testing Datasets¶
We will use Sklearn's train_test_split() to train and test datasets.
The class values in this dataset contain multiple types of heart disease with values ranging from 0 (healthy) to 4 (severe heart disease). We will need to convert our class data to categorical labels. For example, the label 2 will become [0, 0, 1, 0, 0].
# create X and Y datasets for training
from sklearn import model_selection
X = np.array(data.drop(['class'], 1))
y = np.array(data['class'])
X_train, X_test, y_train, y_test = model_selection.train_test_split(X, y, test_size = 0.2)
# convert the data to categorical labels
from keras.utils.np_utils import to_categorical
Y_train = to_categorical(y_train, num_classes=None)
Y_test = to_categorical(y_test, num_classes=None)
print Y_train.shape
print Y_train[:10]
3. Building and Training the Neural Network¶
Begin building a neural network to solve classification problem using keras. We will define a simple neural network with one hidden layer. Since this is a categorical classification problem, we will use a softmax activation function in the final layer of our network and a categorical_crossentropy loss during our training phase.
from keras.models import Sequential
from keras.layers import Dense
from keras.optimizers import Adam
# define a function to build the keras model
def create_model():
# create model
model = Sequential()
model.add(Dense(8, input_dim=13, kernel_initializer='normal', activation='relu'))
model.add(Dense(4, kernel_initializer='normal', activation='relu'))
model.add(Dense(5, activation='softmax'))
# compile model
adam = Adam(lr=0.001)
model.compile(loss='categorical_crossentropy', optimizer=adam, metrics=['accuracy'])
return model
model = create_model()
print(model.summary())
# fit the model to the training data
model.fit(X_train, Y_train, epochs=100, batch_size=10, verbose = 1)
4. Improving Results - A Binary Classification Problem¶
Although we achieved decent results, we still have a fairly large error. This could be because it is very difficult to distinguish between the different severity levels of heart disease (classes 1 - 4). We'll simplify the problem by converting the data to a binary classification problem - heart disease or no heart disease.
# convert into binary classification problem - heart disease or no heart disease
Y_train_binary = y_train.copy()
Y_test_binary = y_test.copy()
Y_train_binary[Y_train_binary > 0] = 1
Y_test_binary[Y_test_binary > 0] = 1
print Y_train_binary[:20]
# define a new keras model for binary classification
def create_binary_model():
# create model
model = Sequential()
model.add(Dense(8, input_dim=13, kernel_initializer='normal', activation='relu'))
model.add(Dense(4, kernel_initializer='normal', activation='relu'))
model.add(Dense(1, activation='sigmoid'))
# Compile model
adam = Adam(lr=0.001)
model.compile(loss='binary_crossentropy', optimizer=adam, metrics=['accuracy'])
return model
binary_model = create_binary_model()
print(binary_model.summary())
# fit the binary model on the training data
binary_model.fit(X_train, Y_train_binary, epochs=100, batch_size=10, verbose = 1)
5. Results and Metrics¶
Let's test the performance of both our categorical model and binary model. To do this, we will make predictions on the training dataset and calculate performance metrics using Sklearn.
# generate classification report using predictions for categorical model
from sklearn.metrics import classification_report, accuracy_score
categorical_pred = np.argmax(model.predict(X_test), axis=1)
print('Results for Categorical Model')
print(accuracy_score(y_test, categorical_pred))
print(classification_report(y_test, categorical_pred))
# generate classification report using predictions for binary model
binary_pred = np.round(binary_model.predict(X_test)).astype(int)
print('Results for Binary Model')
print(accuracy_score(Y_test_binary, binary_pred))
print(classification_report(Y_test_binary, binary_pred))