Life Expectancy¶

We are going to take a quick tour of machine learning by working on an example dataset. The mushroom dataset categorizes mushrooms as 'poisonous' or 'edible' and collects several descriptive properties of each mushroom example.

In [92]:
import pandas as pd
import os
from sklearn.linear_model import LinearRegression
from sklearn.metrics import r2_score
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
In [93]:
pd.options.display.max_rows = 20  # Shows 20 rows
pd.options.display.max_columns = 20  # Shows 20 columns

Loading the dataset¶

In [94]:
# These lines would load the data locally
data_root = "./"
filename = "Life_Expectancy_Data.csv"
filepath = os.path.join(data_root, filename)

# We'll fetch it directly from the web
# data_url = "https://aet-cs.github.io/white/ML/lessons/mushroom.csv"
df = pd.read_csv(filepath)
df
Out[94]:
Country Year Status Life expectancy Adult Mortality infant deaths Alcohol percentage expenditure Hepatitis B Measles ... Polio Total expenditure Diphtheria HIV/AIDS GDP Population thinness 1-19 years thinness 5-9 years Income composition of resources Schooling
0 Afghanistan 2015 Developing 65.0 263.0 62 0.01 71.279624 65.0 1154 ... 6.0 8.16 65.0 0.1 584.259210 33736494.0 17.2 17.3 0.479 10.1
1 Afghanistan 2014 Developing 59.9 271.0 64 0.01 73.523582 62.0 492 ... 58.0 8.18 62.0 0.1 612.696514 327582.0 17.5 17.5 0.476 10.0
2 Afghanistan 2013 Developing 59.9 268.0 66 0.01 73.219243 64.0 430 ... 62.0 8.13 64.0 0.1 631.744976 31731688.0 17.7 17.7 0.470 9.9
3 Afghanistan 2012 Developing 59.5 272.0 69 0.01 78.184215 67.0 2787 ... 67.0 8.52 67.0 0.1 669.959000 3696958.0 17.9 18.0 0.463 9.8
4 Afghanistan 2011 Developing 59.2 275.0 71 0.01 7.097109 68.0 3013 ... 68.0 7.87 68.0 0.1 63.537231 2978599.0 18.2 18.2 0.454 9.5
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
2933 Zimbabwe 2004 Developing 44.3 723.0 27 4.36 0.000000 68.0 31 ... 67.0 7.13 65.0 33.6 454.366654 12777511.0 9.4 9.4 0.407 9.2
2934 Zimbabwe 2003 Developing 44.5 715.0 26 4.06 0.000000 7.0 998 ... 7.0 6.52 68.0 36.7 453.351155 12633897.0 9.8 9.9 0.418 9.5
2935 Zimbabwe 2002 Developing 44.8 73.0 25 4.43 0.000000 73.0 304 ... 73.0 6.53 71.0 39.8 57.348340 125525.0 1.2 1.3 0.427 10.0
2936 Zimbabwe 2001 Developing 45.3 686.0 25 1.72 0.000000 76.0 529 ... 76.0 6.16 75.0 42.1 548.587312 12366165.0 1.6 1.7 0.427 9.8
2937 Zimbabwe 2000 Developing 46.0 665.0 24 1.68 0.000000 79.0 1483 ... 78.0 7.10 78.0 43.5 547.358878 12222251.0 11.0 11.2 0.434 9.8

2938 rows × 22 columns

describe gives a quick overview of each feature

In [95]:
df.describe()
Out[95]:
Year Life expectancy Adult Mortality infant deaths Alcohol percentage expenditure Hepatitis B Measles BMI under-five deaths Polio Total expenditure Diphtheria HIV/AIDS GDP Population thinness 1-19 years thinness 5-9 years Income composition of resources Schooling
count 2938.000000 2928.000000 2928.000000 2938.000000 2744.000000 2938.000000 2385.000000 2938.000000 2904.000000 2938.000000 2919.000000 2712.00000 2919.000000 2938.000000 2490.000000 2.286000e+03 2904.000000 2904.000000 2771.000000 2775.000000
mean 2007.518720 69.224932 164.796448 30.303948 4.602861 738.251295 80.940461 2419.592240 38.321247 42.035739 82.550188 5.93819 82.324084 1.742103 7483.158469 1.275338e+07 4.839704 4.870317 0.627551 11.992793
std 4.613841 9.523867 124.292079 117.926501 4.052413 1987.914858 25.070016 11467.272489 20.044034 160.445548 23.428046 2.49832 23.716912 5.077785 14270.169342 6.101210e+07 4.420195 4.508882 0.210904 3.358920
min 2000.000000 36.300000 1.000000 0.000000 0.010000 0.000000 1.000000 0.000000 1.000000 0.000000 3.000000 0.37000 2.000000 0.100000 1.681350 3.400000e+01 0.100000 0.100000 0.000000 0.000000
25% 2004.000000 63.100000 74.000000 0.000000 0.877500 4.685343 77.000000 0.000000 19.300000 0.000000 78.000000 4.26000 78.000000 0.100000 463.935626 1.957932e+05 1.600000 1.500000 0.493000 10.100000
50% 2008.000000 72.100000 144.000000 3.000000 3.755000 64.912906 92.000000 17.000000 43.500000 4.000000 93.000000 5.75500 93.000000 0.100000 1766.947595 1.386542e+06 3.300000 3.300000 0.677000 12.300000
75% 2012.000000 75.700000 228.000000 22.000000 7.702500 441.534144 97.000000 360.250000 56.200000 28.000000 97.000000 7.49250 97.000000 0.800000 5910.806335 7.420359e+06 7.200000 7.200000 0.779000 14.300000
max 2015.000000 89.000000 723.000000 1800.000000 17.870000 19479.911610 99.000000 212183.000000 87.300000 2500.000000 99.000000 17.60000 99.000000 50.600000 119172.741800 1.293859e+09 27.700000 28.600000 0.948000 20.700000

Data Exploration¶

Show all the columns. Target is 'Life expectancy'

In [96]:
df.columns
Out[96]:
Index(['Country', 'Year', 'Status', 'Life expectancy', 'Adult Mortality',
       'infant deaths', 'Alcohol', 'percentage expenditure', 'Hepatitis B',
       'Measles', 'BMI', 'under-five deaths', 'Polio', 'Total expenditure',
       'Diphtheria', 'HIV/AIDS', 'GDP', 'Population', 'thinness 1-19 years',
       'thinness 5-9 years', 'Income composition of resources', 'Schooling'],
      dtype='object')

Get the size of the dataframe. Shape returns (rows, cols)

In [97]:
df.shape
Out[97]:
(2938, 22)

Let's get all the data types

In [98]:
df.dtypes
Out[98]:
Country                             object
Year                                 int64
Status                              object
Life expectancy                    float64
Adult Mortality                    float64
                                    ...   
Population                         float64
thinness 1-19 years                float64
thinness 5-9 years                 float64
Income composition of resources    float64
Schooling                          float64
Length: 22, dtype: object
In [99]:
df.hist(target)
Out[99]:
array([[<Axes: title={'center': 'Life expectancy'}>]], dtype=object)
No description has been provided for this image

Correlation matrix heat map¶

Let's get a quick visual representation of the relationshop between features in this dataset.

In [100]:
df_heat = df.drop(["Country", "Status"], axis = 1)
In [101]:
corr_matrix = df_heat.corr()
In [104]:
plt.figure(figsize=(16, 6))
# define the mask to set the values in the upper triangle to True
mask = np.triu(np.ones_like(corr_matrix, dtype=np.bool))
heatmap = sns.heatmap(corr_matrix, mask=mask, vmin=-1, vmax=1, annot=True, cmap='BrBG')
heatmap.set_title('Life Expectancy Correlation Heatmap', fontdict={'fontsize':14}, pad=16);
plt.show()
No description has been provided for this image

Which features seem to be important?

In [107]:
row_filter = abs(corr_matrix[target])>0.1
top_features = pd.DataFrame(corr_matrix[target][row_filter])
top_features.sort_values(by=target)
Out[107]:
Life expectancy
Adult Mortality -0.696359
HIV/AIDS -0.556556
thinness 1-19 years -0.477183
thinness 5-9 years -0.471584
under-five deaths -0.222529
infant deaths -0.196557
Measles -0.157586
Year 0.170033
Total expenditure 0.218086
Hepatitis B 0.256762
percentage expenditure 0.381864
Alcohol 0.404877
GDP 0.461455
Polio 0.465556
Diphtheria 0.479495
BMI 0.567694
Income composition of resources 0.724776
Schooling 0.751975
Life expectancy 1.000000

Data Modeling¶

We're finally ready to do some data modeling using scikit-learn. In this cell we import some methods we'll use, reload the data frame (just to be safe), re-pre-process-it, and one-hot-encode all the categorical variables.

In [108]:
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import LabelEncoder
from sklearn.tree import DecisionTreeClassifier
from sklearn.metrics import accuracy_score, classification_report

Linear Regression¶

In [109]:
def get_data(filename):
    df = pd.read_csv(filename)
    return df    
In [110]:
from sklearn.impute import SimpleImputer
from sklearn.compose import ColumnTransformer
from sklearn.impute import SimpleImputer
from sklearn.preprocessing import OneHotEncoder
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import OrdinalEncoder


def pre_process_data(df, one_hot_encode = False):
    target = "Life expectancy"    
    simple_median = SimpleImputer(strategy='median')
    simple_most_freq = SimpleImputer(strategy='most_frequent')
    
    num_cols = df.select_dtypes(include=np.number).columns
    cat_cols = df.select_dtypes(include=object).columns

    df[num_cols] = simple_median.fit_transform(df[num_cols])
    df[cat_cols] = simple_most_freq.fit_transform(df[cat_cols])
    
    # O_encoder = OrdinalEncoder()
    # df[cat_cols]= O_encoder.fit_transform(df[cat_cols])

    if one_hot_encode:
        df = pd.get_dummies(df, dtype=int)
        
    return df
In [111]:
def get_test_train(df, test_size = 0.2, random_state = 42):
    target = "Life expectancy"    
    X = df.drop(target, axis=1)
    y = df[target]
    X_train, X_test, y_train, y_test = train_test_split(X,y,test_size=test_size, random_state=random_state)
    return X_train, X_test, y_train, y_test
In [112]:
df = get_data(filename)
df = pre_process_data(df, one_hot_encode = True)
X_train, X_test, y_train, y_test = get_test_train(df)
In [113]:
clf = LinearRegression()
model = clf.fit(X_train, y_train)

y_pred = clf.predict(X_test)
print(f"Train R-squared = {r2_score(clf.predict(X_train), y_train):5.3}")
print(f"Test R-squared  = {r2_score(y_pred, y_test):5.3}")
Train R-squared = 0.962
Test R-squared  = 0.964
In [114]:
plt.scatter(y_test, y_pred);
plt.plot([40,90],[40,90],color='red')
plt.title("Predicted LE vs. Real LE")
plt.xlabel("True Life Expectancy")
plt.ylabel("Predicted LE")
Out[114]:
Text(0, 0.5, 'Predicted LE')
No description has been provided for this image

Advanced Techniques¶

In [115]:
import matplotlib.pyplot as plt
import pandas as pd

# Assuming `df` is your DataFrame with 20 numerical features and 'LifeExpectancy' as the target variable
target = 'Life expectancy'
df = get_data(filename)
df = pre_process_data(df)
features = df.drop(target, axis=1).select_dtypes(include=['number']).columns

# Set up a grid of subplots
num_features = len(features)
num_cols = 5  # Adjust this to your preference
num_rows = (num_features + num_cols - 1) // num_cols  # Calculates rows needed

plt.figure(figsize=(15, num_rows * 3))

for i, feature in enumerate(features, 1):
    plt.subplot(num_rows, num_cols, i)
    plt.scatter(df[feature], df[target], alpha=0.5)
    plt.title(f'{feature} vs. LE')
    plt.xlabel(feature)
    plt.ylabel(target)

plt.tight_layout()
plt.show()
No description has been provided for this image
In [116]:
df.hist(figsize=(15,15));
No description has been provided for this image

Pre-processing¶

In [117]:
import statsmodels.api as sm

# Add a constant to the model (intercept)

# Fit the OLS model
model = sm.OLS(y_train, X_train).fit()

# Get a summary of the regression
print(model.summary())
                            OLS Regression Results                            
==============================================================================
Dep. Variable:        Life expectancy   R-squared:                       0.963
Model:                            OLS   Adj. R-squared:                  0.960
Method:                 Least Squares   F-statistic:                     267.9
Date:                Wed, 09 Oct 2024   Prob (F-statistic):               0.00
Time:                        13:15:47   Log-Likelihood:                -4758.9
No. Observations:                2350   AIC:                             9938.
Df Residuals:                    2140   BIC:                         1.115e+04
Df Model:                         209                                         
Covariance Type:            nonrobust                                         
================================================================================================================================
                                                                   coef    std err          t      P>|t|      [0.025      0.975]
--------------------------------------------------------------------------------------------------------------------------------
Year                                                             0.2628      0.012     21.916      0.000       0.239       0.286
Adult Mortality                                                 -0.0023      0.001     -4.404      0.000      -0.003      -0.001
infant deaths                                                    0.0780      0.012      6.412      0.000       0.054       0.102
Alcohol                                                         -0.0677      0.027     -2.542      0.011      -0.120      -0.015
percentage expenditure                                           0.0001   5.68e-05      2.340      0.019    2.15e-05       0.000
Hepatitis B                                                     -0.0058      0.002     -2.601      0.009      -0.010      -0.001
Measles                                                      -9.721e-06   4.84e-06     -2.008      0.045   -1.92e-05   -2.26e-07
BMI                                                             -0.0051      0.003     -1.513      0.130      -0.012       0.002
under-five deaths                                               -0.0572      0.008     -6.785      0.000      -0.074      -0.041
Polio                                                            0.0031      0.003      1.203      0.229      -0.002       0.008
Total expenditure                                               -0.0454      0.025     -1.811      0.070      -0.095       0.004
Diphtheria                                                       0.0078      0.003      2.866      0.004       0.002       0.013
HIV/AIDS                                                        -0.3209      0.017    -18.573      0.000      -0.355      -0.287
GDP                                                          -1.317e-05   8.83e-06     -1.492      0.136   -3.05e-05    4.14e-06
Population                                                   -1.166e-09   1.02e-09     -1.138      0.255   -3.18e-09    8.43e-10
thinness 1-19 years                                              0.0204      0.032      0.645      0.519      -0.042       0.082
thinness 5-9 years                                               0.0319      0.032      1.012      0.312      -0.030       0.094
Income composition of resources                                 -0.1747      0.511     -0.342      0.733      -1.177       0.828
Schooling                                                        0.1478      0.046      3.234      0.001       0.058       0.237
Country_Afghanistan                                            -12.5602      0.654    -19.206      0.000     -13.843     -11.278
Country_Albania                                                  4.1251      0.546      7.562      0.000       3.055       5.195
Country_Algeria                                                  1.9191      0.572      3.356      0.001       0.798       3.040
Country_Angola                                                 -19.1966      0.634    -30.267      0.000     -20.440     -17.953
Country_Antigua and Barbuda                                      4.8363      0.613      7.896      0.000       3.635       6.038
Country_Argentina                                                3.8199      0.590      6.479      0.000       2.664       4.976
Country_Armenia                                                  2.4163      0.601      4.018      0.000       1.237       3.596
Country_Australia                                              -11.7984      0.828    -14.243      0.000     -13.423     -10.174
Country_Austria                                                -11.4436      0.922    -12.409      0.000     -13.252      -9.635
Country_Azerbaijan                                              -0.5232      0.536     -0.977      0.329      -1.574       0.527
Country_Bahamas                                                  3.6949      0.627      5.896      0.000       2.466       4.924
Country_Bahrain                                                  4.0994      0.599      6.841      0.000       2.924       5.275
Country_Bangladesh                                              -2.7625      0.704     -3.922      0.000      -4.144      -1.381
Country_Barbados                                                 3.3191      0.612      5.427      0.000       2.120       4.518
Country_Belarus                                                 -0.4641      0.634     -0.732      0.465      -1.708       0.780
Country_Belgium                                                -12.1375      0.887    -13.676      0.000     -13.878     -10.397
Country_Belize                                                  -1.3670      0.576     -2.373      0.018      -2.497      -0.237
Country_Benin                                                  -12.3161      0.594    -20.723      0.000     -13.482     -11.151
Country_Bhutan                                                  -5.6748      0.721     -7.868      0.000      -7.089      -4.260
Country_Bolivia (Plurinational State of)                        -3.0289      0.580     -5.225      0.000      -4.166      -1.892
Country_Bosnia and Herzegovina                                   5.1239      0.611      8.389      0.000       3.926       6.322
Country_Botswana                                                -9.2538      0.582    -15.888      0.000     -10.396      -8.112
Country_Brazil                                                   1.5147      0.631      2.402      0.016       0.278       2.751
Country_Brunei Darussalam                                        4.6145      0.537      8.597      0.000       3.562       5.667
Country_Bulgaria                                               -19.4348      0.925    -21.002      0.000     -21.250     -17.620
Country_Burkina Faso                                           -12.7039      0.750    -16.938      0.000     -14.175     -11.233
Country_Burundi                                                -13.3554      0.638    -20.919      0.000     -14.607     -12.103
Country_Cabo Verde                                               1.3837      0.581      2.381      0.017       0.244       2.523
Country_Cambodia                                                -6.2931      0.614    -10.243      0.000      -7.498      -5.088
Country_Cameroon                                               -13.7371      0.599    -22.928      0.000     -14.912     -12.562
Country_Canada                                                  10.3186      0.646     15.966      0.000       9.051      11.586
Country_Central African Republic                               -18.2718      0.665    -27.468      0.000     -19.576     -16.967
Country_Chad                                                   -17.1495      0.699    -24.536      0.000     -18.520     -15.779
Country_Chile                                                    8.0832      0.595     13.578      0.000       6.916       9.251
Country_China                                                    0.6775      1.005      0.674      0.500      -1.293       2.648
Country_Colombia                                                 2.3495      0.518      4.536      0.000       1.334       3.365
Country_Comoros                                                 -8.9342      0.638    -13.996      0.000     -10.186      -7.682
Country_Congo                                                  -10.2120      0.578    -17.680      0.000     -11.345      -9.079
Country_Cook Islands                                            -0.3522      1.929     -0.183      0.855      -4.135       3.430
Country_Costa Rica                                               7.5549      0.510     14.817      0.000       6.555       8.555
Country_Croatia                                                -16.2245      0.946    -17.148      0.000     -18.080     -14.369
Country_Cuba                                                     6.3740      0.523     12.186      0.000       5.348       7.400
Country_Cyprus                                                 -12.6044      0.931    -13.539      0.000     -14.430     -10.779
Country_Czechia                                                -15.3735      0.987    -15.578      0.000     -17.309     -13.438
Country_Côte d'Ivoire                                          -18.7114      0.621    -30.153      0.000     -19.928     -17.494
Country_Democratic People's Republic of Korea                   -2.3606      0.531     -4.446      0.000      -3.402      -1.319
Country_Democratic Republic of the Congo                       -14.0841      0.704    -20.001      0.000     -15.465     -12.703
Country_Denmark                                                -13.7976      0.859    -16.069      0.000     -15.482     -12.114
Country_Djibouti                                                -8.6067      0.672    -12.802      0.000      -9.925      -7.288
Country_Dominica                                                -0.5753      1.920     -0.300      0.765      -4.341       3.191
Country_Dominican Republic                                       1.6690      0.540      3.091      0.002       0.610       2.728
Country_Ecuador                                                  3.6705      0.518      7.080      0.000       2.654       4.687
Country_Egypt                                                   -0.0465      0.604     -0.077      0.939      -1.232       1.139
Country_El Salvador                                              0.6517      0.536      1.216      0.224      -0.400       1.703
Country_Equatorial Guinea                                      -12.8233      0.633    -20.267      0.000     -14.064     -11.582
Country_Eritrea                                                 -9.2433      0.669    -13.826      0.000     -10.554      -7.932
Country_Estonia                                                  3.7999      0.638      5.960      0.000       2.550       5.050
Country_Ethiopia                                                -7.9965      0.686    -11.649      0.000      -9.343      -6.650
Country_Fiji                                                    -2.9123      0.576     -5.053      0.000      -4.043      -1.782
Country_Finland                                                  9.4469      0.584     16.165      0.000       8.301      10.593
Country_France                                                  10.8405      0.672     16.124      0.000       9.522      12.159
Country_Gabon                                                   -5.7206      0.571    -10.017      0.000      -6.841      -4.601
Country_Gambia                                                 -10.2851      0.564    -18.248      0.000     -11.390      -9.180
Country_Georgia                                                  2.5948      0.535      4.848      0.000       1.545       3.644
Country_Germany                                                -11.6530      0.891    -13.086      0.000     -13.399      -9.907
Country_Ghana                                                   -8.8819      0.622    -14.290      0.000     -10.101      -7.663
Country_Greece                                                  10.6086      0.662     16.018      0.000       9.310      11.907
Country_Grenada                                                  1.6641      0.656      2.537      0.011       0.378       2.950
Country_Guatemala                                                1.6711      0.588      2.843      0.005       0.518       2.824
Country_Guinea                                                 -13.2949      0.667    -19.928      0.000     -14.603     -11.987
Country_Guinea-Bissau                                          -13.7809      0.658    -20.955      0.000     -15.071     -12.491
Country_Guyana                                                  -4.4222      0.587     -7.534      0.000      -5.573      -3.271
Country_Haiti                                                   -9.4562      0.618    -15.312      0.000     -10.667      -8.245
Country_Honduras                                                 2.4061      0.542      4.436      0.000       1.342       3.470
Country_Hungary                                                -18.5916      0.880    -21.119      0.000     -20.318     -16.865
Country_Iceland                                                -10.9866      0.830    -13.242      0.000     -12.614      -9.359
Country_India                                                   -8.7540      2.657     -3.295      0.001     -13.965      -3.543
Country_Indonesia                                               -4.3764      0.720     -6.076      0.000      -5.789      -2.964
Country_Iran (Islamic Republic of)                               2.2397      0.661      3.390      0.001       0.944       3.535
Country_Iraq                                                    -0.6459      0.566     -1.140      0.254      -1.757       0.465
Country_Ireland                                                -13.0366      0.854    -15.262      0.000     -14.712     -11.361
Country_Israel                                                   9.8839      0.542     18.237      0.000       8.821      10.947
Country_Italy                                                  -10.2338      0.897    -11.414      0.000     -11.992      -8.476
Country_Jamaica                                                  3.7132      0.519      7.154      0.000       2.695       4.731
Country_Japan                                                  -10.7261      0.915    -11.719      0.000     -12.521      -8.931
Country_Jordan                                                   1.6096      0.628      2.565      0.010       0.379       2.840
Country_Kazakhstan                                              -4.1239      0.530     -7.783      0.000      -5.163      -3.085
Country_Kenya                                                   -9.8681      0.701    -14.078      0.000     -11.243      -8.494
Country_Kiribati                                                -5.8018      0.560    -10.359      0.000      -6.900      -4.703
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Status_Developed                                              -436.0261     22.964    -18.987      0.000    -481.060    -390.992
Status_Developing                                             -457.7453     23.650    -19.355      0.000    -504.125    -411.365
==============================================================================
Omnibus:                      570.909   Durbin-Watson:                   1.911
Prob(Omnibus):                  0.000   Jarque-Bera (JB):            16400.405
Skew:                           0.503   Prob(JB):                         0.00
Kurtosis:                      15.903   Cond. No.                     8.21e+24
==============================================================================

Notes:
[1] Standard Errors assume that the covariance matrix of the errors is correctly specified.
[2] The smallest eigenvalue is 8.56e-32. This might indicate that there are
strong multicollinearity problems or that the design matrix is singular.
In [56]:
# Extract the summary table as a DataFrame
summary_table = model.summary2().tables[1]  # tables[1] is the coefficients table in summary2()

# Sort by p-values (for example)
sorted_summary = summary_table.sort_values(by='t')


# Set display options to prevent truncation
pd.options.display.max_rows = None  # Shows all rows
pd.options.display.max_columns = None  # Shows all columns

sorted_summary
Out[56]:
Coef. Std.Err. t P>|t| [0.025 0.975]
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In [ ]: