Machine Learning Using Python (MEAFA Workshop)

Lesson 10: Neural Networks (Classification)

This notebook relies on the following libraries and settings.

In [1]:
# Packages
import numpy as np
from scipy import stats
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import warnings
warnings.filterwarnings('ignore')

In [2]:
# Plot settings
sns.set_context('notebook')
sns.set_style('ticks')
colours = ['#1F77B4', '#FF7F0E', '#2CA02C', '#DB2728', '#9467BD', '#8C564B', '#E377C2','#7F7F7F', '#BCBD22', '#17BECF']
crayon = ['#4E79A7','#F28E2C','#E15759','#76B7B2','#59A14F', '#EDC949','#AF7AA1','#FF9DA7','#9C755F','#BAB0AB']
sns.set_palette(colours)
%matplotlib inline
plt.rcParams['figure.figsize'] = (9, 6)

In [3]:
from sklearn.linear_model import LogisticRegression

from sklearn.model_selection import train_test_split
from sklearn.model_selection import GridSearchCV, RandomizedSearchCV
from sklearn.metrics import accuracy_score, confusion_matrix, roc_auc_score
from sklearn.metrics import precision_score, average_precision_score, log_loss

from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import Pipeline


Work Analytics Data¶

We use the Human Resources Analytics data available from Kaggle Datasets.

Business objective: To predict which employees will leave the company.

In [4]:
data = pd.read_csv('Datasets/HR.csv')
data = data.rename(columns = {'sales' : 'role'})

Out[4]:
satisfaction_level last_evaluation number_project average_montly_hours time_spend_company Work_accident left promotion_last_5years role salary
0 0.38 0.53 2 157 3 0 1 0 sales low
1 0.80 0.86 5 262 6 0 1 0 sales medium
2 0.11 0.88 7 272 4 0 1 0 sales medium
3 0.72 0.87 5 223 5 0 1 0 sales low
4 0.37 0.52 2 159 3 0 1 0 sales low
In [5]:
response='left'
predictors = list(data.columns.values)
predictors.remove(response)

index_train, index_test  = train_test_split(np.array(data.index), stratify=data[response], train_size=0.2, random_state=5)

train = data.loc[index_train,].copy()
test =  data.loc[index_test,:].copy()

y_train = train[response]
y_test = test[response]


Before estimating the models, we need to convert the categorical variables into binary variables.

In [6]:
dummies = pd.get_dummies(data['role'], drop_first=True)
data = data.join(dummies)
data = data.drop('role', axis= 1)

dummies = pd.get_dummies(data['salary'],  prefix = 'salary', drop_first=True)
data = data.join(dummies)
data = data.drop('salary', axis= 1)


We then update our list of predictors accordingly and construct the train and test design matrices.

In [7]:
train = data.loc[index_train,].copy()
test =  data.loc[index_test,:].copy()

predictors = list(train.columns.values)
predictors.remove(response)

X_train = data.loc[index_train, predictors].copy()

scaler = StandardScaler()
scaler.fit(X_train)

X_train = scaler.transform(X_train)
X_test = scaler.transform(test[predictors].values)

X_train.shape

Out[7]:
(2999, 18)

Neural Networks¶

In [8]:
from keras.models import Sequential
from keras.layers import Dense
from keras.layers import Dropout
from keras.layers import Activation

Using TensorFlow backend.


Two Hidden Layers¶

In [9]:
mlp = Sequential()
mlp.add(Dense(128, input_dim=X_train.shape[1], init='uniform', activation='relu'))
mlp.fit(X_train, y_train, epochs=500, verbose=0)

Out[9]:
<keras.callbacks.History at 0x22f1e4cb898>

Dropout¶

In [10]:
model = Sequential()
model.add(Dense(128, input_dim=X_train.shape[1], init='uniform', activation='relu'))
model.fit(X_train, y_train, epochs=500, verbose=0)

Out[10]:
<keras.callbacks.History at 0x22f1ed35e80>

Model Evaluation¶

We estimate a logistic regression as a benchmark.

In [11]:
logit = LogisticRegression(C=1e5)
logit.fit(X_train, y_train)

Out[11]:
LogisticRegression(C=100000.0, class_weight=None, dual=False,
fit_intercept=True, intercept_scaling=1, max_iter=100,
multi_class='ovr', n_jobs=1, penalty='l2', random_state=None,
solver='liblinear', tol=0.0001, verbose=0, warm_start=False)
In [12]:
columns=['Error rate', 'Sensitivity', 'Specificity', 'AUC', 'Precision']
rows=['Logistic regression', 'Neural Net', 'Neural Net (dropout)']
results=pd.DataFrame(0.0, columns=columns, index=rows)

methods=[logit, mlp, model]

for i, method in enumerate(methods):

y_pred = method.predict(X_test)
if method != logit:
y_prob = y_pred
y_pred = (y_pred>0.5).astype(int)
else:
y_prob = method.predict_proba(X_test)[:,1]

confusion  = confusion_matrix(y_test, y_pred)
results.iloc[i,0]=  1 - accuracy_score(y_test, y_pred)
results.iloc[i,1]=  confusion[1,1]/np.sum(confusion[1,:])
results.iloc[i,2]=  confusion[0,0]/np.sum(confusion[0,:])
results.iloc[i,4]=  precision_score(y_test, y_pred)
results.iloc[i,3] = roc_auc_score(y_test, y_prob)

results.round(3)

Out[12]:
Error rate Sensitivity Specificity AUC Precision
Logistic regression 0.225 0.279 0.930 0.822 0.556
Neural Net 0.039 0.922 0.973 0.972 0.915
Neural Net (dropout) 0.034 0.913 0.982 0.974 0.941