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Demo on the capability of Yandex CatBoost gradient boosting classifier on a fictitious IBM HR dataset obtained from Kaggle. Data exploration, cleaning, preprocessing and model tuning are performed on the dataset

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Exploration of Yandex CatBoost in Python

This demo will provide a brief introduction in

  • performing data exploration and preprocessing
  • feature subset selection: low variance filter
  • feature subset selection: high correlation filter
  • catboost model tuning
  • importance of data preprocessing: data normalization
  • exploration of catboost's feature importance ranking

Getting started

Open YandexCatBoost-Demo.ipynb on a jupyter notebook environment, or Google colab. The notebook consists of further technical details.

Future Improvements

Results from the feature importance ranking shows that attribute ‘MaritalStatus’ impacts minimally in class label prediction and could potential be a noise attribute. Removing it might increase model’s accuracy.

Codes Walkthrough

Installing the open source Yandex CatBoost package

pip install catboost

Importing the required packaged: Numpy, Pandas, Matplotlib, Seaborn, Scikit-learn and CatBoost

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
# plt.style.use('ggplot') 
import seaborn as sns
from catboost import Pool, CatBoostClassifier, cv, CatboostIpythonWidget
from sklearn.preprocessing import MinMaxScaler
from sklearn.feature_selection import VarianceThreshold

Loading of IBM HR Dataset into pandas dataframe

ibm_hr_df = pd.read_csv("IBM-HR-Employee-Attrition.csv")

Part 1a: Data Exploration - Summary Statistics

Getting the summary statistics of the IBM HR dataset

ibm_hr_df.describe()
Age DailyRate DistanceFromHome Education EmployeeCount EmployeeNumber EnvironmentSatisfaction HourlyRate JobInvolvement JobLevel ... RelationshipSatisfaction StandardHours StockOptionLevel TotalWorkingYears TrainingTimesLastYear WorkLifeBalance YearsAtCompany YearsInCurrentRole YearsSinceLastPromotion YearsWithCurrManager
count 1470.000000 1470.000000 1470.000000 1470.000000 1470.0 1470.000000 1470.000000 1470.000000 1470.000000 1470.000000 ... 1470.000000 1470.0 1470.000000 1470.000000 1470.000000 1470.000000 1470.000000 1470.000000 1470.000000 1470.000000
mean 36.923810 802.485714 9.192517 2.912925 1.0 1024.865306 2.721769 65.891156 2.729932 2.063946 ... 2.712245 80.0 0.793878 11.279592 2.799320 2.761224 7.008163 4.229252 2.187755 4.123129
std 9.135373 403.509100 8.106864 1.024165 0.0 602.024335 1.093082 20.329428 0.711561 1.106940 ... 1.081209 0.0 0.852077 7.780782 1.289271 0.706476 6.126525 3.623137 3.222430 3.568136
min 18.000000 102.000000 1.000000 1.000000 1.0 1.000000 1.000000 30.000000 1.000000 1.000000 ... 1.000000 80.0 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000
25% 30.000000 465.000000 2.000000 2.000000 1.0 491.250000 2.000000 48.000000 2.000000 1.000000 ... 2.000000 80.0 0.000000 6.000000 2.000000 2.000000 3.000000 2.000000 0.000000 2.000000
50% 36.000000 802.000000 7.000000 3.000000 1.0 1020.500000 3.000000 66.000000 3.000000 2.000000 ... 3.000000 80.0 1.000000 10.000000 3.000000 3.000000 5.000000 3.000000 1.000000 3.000000
75% 43.000000 1157.000000 14.000000 4.000000 1.0 1555.750000 4.000000 83.750000 3.000000 3.000000 ... 4.000000 80.0 1.000000 15.000000 3.000000 3.000000 9.000000 7.000000 3.000000 7.000000
max 60.000000 1499.000000 29.000000 5.000000 1.0 2068.000000 4.000000 100.000000 4.000000 5.000000 ... 4.000000 80.0 3.000000 40.000000 6.000000 4.000000 40.000000 18.000000 15.000000 17.000000

8 rows × 26 columns

Zooming in on the summary statistics of irrelevant attributes EmployeeCount and StandardHours

irrList = ['EmployeeCount', 'StandardHours'] 
ibm_hr_df[irrList].describe()
EmployeeCount StandardHours
count 1470.0 1470.0
mean 1.0 80.0
std 0.0 0.0
min 1.0 80.0
25% 1.0 80.0
50% 1.0 80.0
75% 1.0 80.0
max 1.0 80.0

Zooming in on the summary statistics of irrelevant attribute Over18

ibm_hr_df["Over18"].value_counts()
Y    1470
Name: Over18, dtype: int64

From the summary statistics, one could see that attributes EmployeeCount, StandardHours and Over18 holds only one single value for all of the 1470 records

EmployeeCount only holds a single value - 1.0
StandardHours only holds a single value - 80.0
Over18 only holds a single value - 'Y'

These irrelevant attributes are duely dropped from the dataset

Part 1b: Data Exploration - Missing Values and Duplicate Records

Checking for 'NA' and missing values in the dataset.

ibm_hr_df.isnull().sum(axis=0)
Age                         0
Attrition                   0
BusinessTravel              0
DailyRate                   0
Department                  0
DistanceFromHome            0
Education                   0
EducationField              0
EmployeeCount               0
EmployeeNumber              0
EnvironmentSatisfaction     0
Gender                      0
HourlyRate                  0
JobInvolvement              0
JobLevel                    0
JobRole                     0
JobSatisfaction             0
MaritalStatus               0
MonthlyIncome               0
MonthlyRate                 0
NumCompaniesWorked          0
Over18                      0
OverTime                    0
PercentSalaryHike           0
PerformanceRating           0
RelationshipSatisfaction    0
StandardHours               0
StockOptionLevel            0
TotalWorkingYears           0
TrainingTimesLastYear       0
WorkLifeBalance             0
YearsAtCompany              0
YearsInCurrentRole          0
YearsSinceLastPromotion     0
YearsWithCurrManager        0
dtype: int64

Well, we got lucky here, there isn't any missing values in this dataset

Next, let's check for the existence of duplicate records in the dataset

ibm_hr_df.duplicated().sum()
0

There are also no duplicate records in the dataset

Converting OverTime binary categorical attribute to {1, 0}

ibm_hr_df['OverTime'].replace(to_replace=dict(Yes=1, No=0), inplace=True)

Part 2a: Data Preprocessing - Removal of Irrelevant Attributes

ibm_hr_df = ibm_hr_df.drop(['EmployeeCount', 'StandardHours', 'Over18'], axis=1)

Part 2b: Data Preprocessing - Feature Subset Selection - Low Variance Filter

Performing variance analysis to aid in feature selection

variance_x = ibm_hr_df.drop('Attrition', axis=1)
variance_one_hot = pd.get_dummies(variance_x)
#Normalise the dataset. This is required for getting the variance threshold
scaler = MinMaxScaler()
scaler.fit(variance_one_hot)
MinMaxScaler(copy=True, feature_range=(0, 1))
scaled_variance_one_hot = scaler.transform(variance_one_hot)
#Set the threshold values and run VarianceThreshold 
thres = .85* (1 - .85)
sel = VarianceThreshold(threshold=thres)
sel.fit(scaled_variance_one_hot)
variance = sel.variances_
#Sorting of the score in acsending orders for plotting
indices = np.argsort(variance)[::-1]
feature_list = list(variance_one_hot)
sorted_feature_list = []
thres_list = []
for f in range(len(variance_one_hot.columns)):
    sorted_feature_list.append(feature_list[indices[f]])
    thres_list.append(thres)
plt.figure(figsize=(14,6))
plt.title("Feature Variance: %f" %(thres), fontsize = 14)
plt.bar(range(len(variance_one_hot.columns)), variance[indices], color="c")
plt.xticks(range(len(variance_one_hot.columns)), sorted_feature_list, rotation = 90)
plt.xlim([-0.5, len(variance_one_hot.columns)])
plt.plot(range(len(variance_one_hot.columns)), thres_list, "k-", color="r")
plt.tight_layout()
plt.show()

png

Part 2c: Data Preprocessing - Feature Subset Selection - High Correlation Filter

Performing Pearson correlation analysis between attributes to aid in feature selection

plt.figure(figsize=(16,16))
sns.heatmap(ibm_hr_df.corr(), annot=True, fmt=".2f")

plt.show()

png

Part 3: Mutli-Class Label Generation

rAttrList = ['Department', 'OverTime', 'HourlyRate',
             'StockOptionLevel', 'DistanceFromHome',
             'YearsInCurrentRole', 'Age']
#keep only the attribute list on rAttrList
label_hr_df = ibm_hr_df[rAttrList]
#convert continous attribute DistanceFromHome to Catergorical
#: 1: near, 2: mid distance, 3: far
maxValues = label_hr_df['DistanceFromHome'].max()
minValues = label_hr_df['DistanceFromHome'].min()
intervals = (maxValues - minValues)/3
bins = [0, (minValues + intervals), (maxValues - intervals), maxValues]
groupName = [1, 2, 3]
label_hr_df['CatDistanceFromHome'] = pd.cut(label_hr_df['DistanceFromHome'], bins, labels = groupName)
# convert col type from cat to int64
label_hr_df['CatDistanceFromHome'] = pd.to_numeric(label_hr_df['CatDistanceFromHome']) 
label_hr_df.drop(['DistanceFromHome'], axis = 1, inplace = True)
#replace department into 0 & 1, 0: R&D, and 1: Non-R&D
label_hr_df['Department'].replace(['Research & Development', 'Human Resources', 'Sales'],
                                  [0, 1, 1], inplace = True)
#normalise data
label_hr_df_norm = (label_hr_df - label_hr_df.min()) / (label_hr_df.max() - label_hr_df.min())
#create a data frame for the function value and class labels
value_df = pd.DataFrame(columns = ['ClassValue'])
#compute the class value
for row in range (0, ibm_hr_df.shape[0]):
    if label_hr_df_norm['Department'][row] == 0:
        value = 0.3 * label_hr_df_norm['HourlyRate'][row] - 0.2 * label_hr_df_norm['OverTime'][row] + \
            - 0.2 * label_hr_df_norm['CatDistanceFromHome'][row] + 0.15 * label_hr_df_norm['StockOptionLevel'][row] + \
            0.1 * label_hr_df_norm['Age'][row] - 0.05 * label_hr_df_norm['YearsInCurrentRole'][row]
    
    else:
        value = 0.2 * label_hr_df_norm['HourlyRate'][row] - 0.3 * label_hr_df_norm['OverTime'][row] + \
            - 0.15 * label_hr_df_norm['CatDistanceFromHome'][row] + 0.2 * label_hr_df_norm['StockOptionLevel'][row] + \
            0.05 * label_hr_df_norm['Age'][row] - 0.1 * label_hr_df_norm['YearsInCurrentRole'][row]
    value_df.loc[row] = value
# top 500 highest class value is satisfied with their job
v1 = value_df.sort_values('ClassValue', ascending = False).reset_index(drop = True)\
        ['ClassValue'][499]
# next top 500 is neutral
v2 = value_df.sort_values('ClassValue', ascending = False).reset_index(drop = True)\
        ['ClassValue'][999]
# rest is unsatisfied
label_df = pd.DataFrame(columns = ['ClassLabel'])
#compute the classlabel
for row in range (0, value_df.shape[0]):
    if value_df['ClassValue'][row] >= v1:
        cat = "Satisfied"
    elif value_df['ClassValue'][row] >= v2:
        cat = "Neutral"
    else:
        cat = "Unsatisfied"
    label_df.loc[row] = cat
df = pd.concat([ibm_hr_df, label_df], axis = 1)

Part 4: Classification with CatBoost

df = df[['Age', 'Department', 'DistanceFromHome', 'HourlyRate', 'OverTime', 'StockOptionLevel', 
         'MaritalStatus', 'YearsInCurrentRole', 'EmployeeNumber', 'ClassLabel']]

Split dataset into attributes/features X and label/class y

X = df.drop('ClassLabel', axis=1)
y = df.ClassLabel

Replacing label/class value from 'Satisfied', 'Neutral' and 'Unsatisfied' to 2, 1 and 0

y.replace(to_replace=dict(Satisfied=2, Neutral=1, Unsatisfied=0), inplace=True)

Performing 'one hot encoding' method

one_hot = pd.get_dummies(X)
categorical_features_indices = np.where(one_hot.dtypes != np.float)[0]

Part 5: Model training with CatBoost

Now lets split our data to train (70%) and test (30%) set:

from sklearn.model_selection import train_test_split

X_train, X_test, y_train, y_test = train_test_split(one_hot, y, train_size=0.7, random_state=1234)
model = CatBoostClassifier(
    custom_loss = ['Accuracy'],
    random_seed = 100,
    loss_function = 'MultiClass'
)
model.fit(
    X_train, y_train,
    cat_features = categorical_features_indices,
    verbose = True,  # you can uncomment this for text output
    #plot = True
)
cm = pd.DataFrame()
cm['Satisfaction'] = y_test
cm['Predict'] = model.predict(X_test)
mappingSatisfaction = {0:'Unsatisfied', 1: 'Neutral', 2: 'Satisfied'}
mappingPredict = {0.0:'Unsatisfied', 1.0: 'Neutral', 2.0: 'Satisfied'}
cm = cm.replace({'Satisfaction': mappingSatisfaction, 'Predict': mappingPredict})
pd.crosstab(cm['Satisfaction'], cm['Predict'], margins=True)
Predict Neutral Satisfied Unsatisfied All
Satisfaction
Neutral 143 8 8 159
Satisfied 20 123 1 144
Unsatisfied 18 0 120 138
All 181 131 129 441 
model.score(X_test, y_test)
0.87528344671201819

Part 6: CatBoost Classifier Tuning

model = CatBoostClassifier(
    l2_leaf_reg = 5,
    iterations = 1000,
    fold_len_multiplier = 1.1,
    custom_loss = ['Accuracy'],
    random_seed = 100,
    loss_function = 'MultiClass'
)
model.fit(
    X_train, y_train,
    cat_features = categorical_features_indices,
    verbose = True,  # you can uncomment this for text output
    #plot = True
)
cm = pd.DataFrame()
cm['Satisfaction'] = y_test
cm['Predict'] = model.predict(X_test)
mappingSatisfaction = {0:'Unsatisfied', 1: 'Neutral', 2: 'Satisfied'}
mappingPredict = {0.0:'Unsatisfied', 1.0: 'Neutral', 2.0: 'Satisfied'}
cm = cm.replace({'Satisfaction': mappingSatisfaction, 'Predict': mappingPredict})
pd.crosstab(cm['Satisfaction'], cm['Predict'], margins=True)
Predict Neutral Satisfied Unsatisfied All
Satisfaction
Neutral 142 9 8 159
Satisfied 17 126 1 144
Unsatisfied 12 0 126 138
All 171 135 135 441 
model.score(X_test, y_test)
0.89342403628117917

Part 7: Data Preprocessing: Attributes Value Normalization

Normalization of features, after realizing that tuning no longer improve model's accuracy

one_hot = (one_hot - one_hot.mean()) / (one_hot.max() - one_hot.min())
categorical_features_indices = np.where(one_hot.dtypes != np.float)[0]
from sklearn.model_selection import train_test_split

X_train, X_test, y_train, y_test = train_test_split(one_hot, y, train_size=0.7, random_state=1234)
model = CatBoostClassifier(
    l2_leaf_reg = 5,
    iterations = 1000,
    fold_len_multiplier = 1.1,
    custom_loss = ['Accuracy'],
    random_seed = 100,
    loss_function = 'MultiClass'
)
model.fit(
    X_train, y_train,
    cat_features = categorical_features_indices,
    verbose = True,  # you can uncomment this for text output
    #plot = True
)
feature_score = pd.DataFrame(list(zip(one_hot.dtypes.index, model.get_feature_importance(Pool(one_hot, label=y, cat_features=categorical_features_indices)))),
                columns=['Feature','Score'])
feature_score = feature_score.sort_values(by='Score', ascending=False, inplace=False, kind='quicksort', na_position='last')
plt.rcParams["figure.figsize"] = (12,7)
ax = feature_score.plot('Feature', 'Score', kind='bar', color='c')
ax.set_title("Catboost Feature Importance Ranking", fontsize = 14)
ax.set_xlabel('')

rects = ax.patches

# get feature score as labels round to 2 decimal
labels = feature_score['Score'].round(2)

for rect, label in zip(rects, labels):
    height = rect.get_height()
    ax.text(rect.get_x() + rect.get_width()/2, height + 0.35, label, ha='center', va='bottom')

plt.show()

png

cm = pd.DataFrame()
cm['Satisfaction'] = y_test
cm['Predict'] = model.predict(X_test)
mappingSatisfaction = {0:'Unsatisfied', 1: 'Neutral', 2: 'Satisfied'}
mappingPredict = {0.0:'Unsatisfied', 1.0: 'Neutral', 2.0: 'Satisfied'}
cm = cm.replace({'Satisfaction': mappingSatisfaction, 'Predict': mappingPredict})
pd.crosstab(cm['Satisfaction'], cm['Predict'], margins=True)
Predict Neutral Satisfied Unsatisfied All
Satisfaction
Neutral 146 11 2 159
Satisfied 7 137 0 144
Unsatisfied 8 0 130 138
All 161 148 132 441 
model.score(X_test, y_test)
0.93650793650793651

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Demo on the capability of Yandex CatBoost gradient boosting classifier on a fictitious IBM HR dataset obtained from Kaggle. Data exploration, cleaning, preprocessing and model tuning are performed on the dataset

Topics

visualization python data-science pandas seaborn feature-selection data-analysis data-preprocessing python27 gradient-boosting-classifier gradient-boosting pearson-correlation one-hot-encode catboost variance-analysis yandex-catboost

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