In [ ]: #Week-1

In [2]: import numpy as np

import pandas as pd
import matplotlib.pyplot as plt
from matplotlib import style
import seaborn as sns
%matplotlib inline

In [13]: df = pd.read_csv('F:\Data Science\Simplilearn\Capstone/Project 2\Healthcare - Diabetes\health c

In [14]: df.head()

Out[14]: Pregnancies Glucose BloodPressure SkinThickness Insulin BMI DiabetesPedigreeFunction Age Outcome

0 6 148 72 35 0 33.6 0.627 50 1

1 1 85 66 29 0 26.6 0.351 31 0

2 8 183 64 0 0 23.3 0.672 32 1

3 1 89 66 23 94 28.1 0.167 21 0

4 0 137 40 35 168 43.1 2.288 33 1

In [16]: df.isnull().any()

Out[16]: Pregnancies False

Glucose False
BloodPressure False
SkinThickness False
Insulin False
BMI False
DiabetesPedigreeFunction False
Age False
Outcome False
dtype: bool

In [17]: df.info()

<class 'pandas.core.frame.DataFrame'>
RangeIndex: 768 entries, 0 to 767
Data columns (total 9 columns):
# Column Non-Null Count Dtype
--- ------ -------------- -----
0 Pregnancies 768 non-null int64
1 Glucose 768 non-null int64
2 BloodPressure 768 non-null int64
3 SkinThickness 768 non-null int64
4 Insulin 768 non-null int64
5 BMI 768 non-null float64
6 DiabetesPedigreeFunction 768 non-null float64
7 Age 768 non-null int64
8 Outcome 768 non-null int64
dtypes: float64(2), int64(7)
memory usage: 54.1 KB

In [18]: Positive = df[df['Outcome']==1]

Positive.head(5)

Out[18]: Pregnancies Glucose BloodPressure SkinThickness Insulin BMI DiabetesPedigreeFunction Age Outcome

0 6 148 72 35 0 33.6 0.627 50 1

2 8 183 64 0 0 23.3 0.672 32 1

4 0 137 40 35 168 43.1 2.288 33 1

6 3 78 50 32 88 31.0 0.248 26 1
 Pregnancies Glucose BloodPressure SkinThickness Insulin BMI DiabetesPedigreeFunction Age Outcome

8 2 197 70 45 543 30.5 0.158 53 1

In [26]: df['Glucose'].value_counts().head(5)

Out[26]: 100 17
99 17
129 14
125 14
111 14
Name: Glucose, dtype: int64

In [20]: plt.hist(df['Glucose'])

Out[20]: (array([ 5., 0., 4., 32., 156., 211., 163., 95., 56., 46.]),
array([ 0. , 19.9, 39.8, 59.7, 79.6, 99.5, 119.4, 139.3, 159.2,
179.1, 199. ]),
<BarContainer object of 10 artists>)

In [27]: df['BloodPressure'].value_counts().head()

Out[27]: 70 57
74 52
68 45
78 45
72 44
Name: BloodPressure, dtype: int64

In [22]: plt.hist(df['BloodPressure'])

Out[22]: (array([ 35., 1., 2., 13., 107., 261., 243., 87., 14., 5.]),
array([ 0. , 12.2, 24.4, 36.6, 48.8, 61. , 73.2, 85.4, 97.6,
109.8, 122. ]),
<BarContainer object of 10 artists>)

In [28]: df['SkinThickness'].value_counts().head()
Out[28]: 0 227
32 31
30 27
27 23
23 22
Name: SkinThickness, dtype: int64

In [24]: plt.hist(df['SkinThickness'])

Out[24]: (array([231., 107., 165., 175., 78., 9., 2., 0., 0., 1.]),
array([ 0. , 9.9, 19.8, 29.7, 39.6, 49.5, 59.4, 69.3, 79.2, 89.1, 99. ]),
<BarContainer object of 10 artists>)

In [29]: df['Insulin'].value_counts().head()

Out[29]: 0 374
105 11
140 9
130 9
120 8
Name: Insulin, dtype: int64

In [30]: plt.hist(df['Insulin'])

Out[30]: (array([487., 155., 70., 30., 8., 9., 5., 1., 2., 1.]),
array([ 0. , 84.6, 169.2, 253.8, 338.4, 423. , 507.6, 592.2, 676.8,
761.4, 846. ]),
<BarContainer object of 10 artists>)

In [31]: df['BMI'].value_counts().head()

Out[31]: 32.0 13
31.6 12
31.2 12
0.0 11
33.3 10
Name: BMI, dtype: int64

In [32]: plt.hist(df['BMI'])
Out[32]: (array([ 11., 0., 15., 156., 268., 224., 78., 12., 3., 1.]),
array([ 0. , 6.71, 13.42, 20.13, 26.84, 33.55, 40.26, 46.97, 53.68,
60.39, 67.1 ]),
<BarContainer object of 10 artists>)

In [33]: df.describe().transpose()

Out[33]: count mean std min 25% 50% 75% max

Pregnancies 768.0 3.845052 3.369578 0.000 1.00000 3.0000 6.00000 17.00

Glucose 768.0 120.894531 31.972618 0.000 99.00000 117.0000 140.25000 199.00

BloodPressure 768.0 69.105469 19.355807 0.000 62.00000 72.0000 80.00000 122.00

SkinThickness 768.0 20.536458 15.952218 0.000 0.00000 23.0000 32.00000 99.00

Insulin 768.0 79.799479 115.244002 0.000 0.00000 30.5000 127.25000 846.00

BMI 768.0 31.992578 7.884160 0.000 27.30000 32.0000 36.60000 67.10

DiabetesPedigreeFunction 768.0 0.471876 0.331329 0.078 0.24375 0.3725 0.62625 2.42

Age 768.0 33.240885 11.760232 21.000 24.00000 29.0000 41.00000 81.00

Outcome 768.0 0.348958 0.476951 0.000 0.00000 0.0000 1.00000 1.00

In [34]: #Week-2

In [36]: plt.hist(Positive['BMI'],histtype='stepfilled',bins=20)

Out[36]: (array([ 2., 0., 0., 0., 0., 0., 3., 13., 38., 61., 61., 36., 27.,
14., 7., 3., 1., 1., 0., 1.]),
array([ 0. , 3.355, 6.71 , 10.065, 13.42 , 16.775, 20.13 , 23.485,
26.84 , 30.195, 33.55 , 36.905, 40.26 , 43.615, 46.97 , 50.325,
53.68 , 57.035, 60.39 , 63.745, 67.1 ]),
[<matplotlib.patches.Polygon at 0x1180d540b20>])
In [37]: Positive['BMI'].value_counts().head()

Out[37]: 32.9 8
31.6 7
33.3 6
30.5 5
32.0 5
Name: BMI, dtype: int64

In [38]: plt.hist(Positive['Glucose'],histtype='stepfilled',bins=20)

Out[38]: (array([ 2., 0., 0., 0., 0., 0., 0., 1., 4., 9., 28., 26., 36.,
27., 29., 22., 24., 21., 25., 14.]),
array([ 0. , 9.95, 19.9 , 29.85, 39.8 , 49.75, 59.7 , 69.65,
79.6 , 89.55, 99.5 , 109.45, 119.4 , 129.35, 139.3 , 149.25,
159.2 , 169.15, 179.1 , 189.05, 199. ]),
[<matplotlib.patches.Polygon at 0x1180d59bfa0>])

In [39]: Positive['Glucose'].value_counts().head()

Out[39]: 125 7
158 6
128 6
115 6
129 6
Name: Glucose, dtype: int64

In [40]: plt.hist(Positive['BloodPressure'],histtype='stepfilled',bins=20)

Out[40]: (array([16., 0., 0., 0., 0., 1., 0., 1., 6., 6., 19., 37., 56.,
36., 41., 31., 7., 4., 4., 3.]),
array([ 0. , 5.7, 11.4, 17.1, 22.8, 28.5, 34.2, 39.9, 45.6,
51.3, 57. , 62.7, 68.4, 74.1, 79.8, 85.5, 91.2, 96.9,
102.6, 108.3, 114. ]),
[<matplotlib.patches.Polygon at 0x1180d600b80>])

In [41]: Positive['BloodPressure'].value_counts().head()
Out[41]: 70 23
76 18
78 17
74 17
72 16
Name: BloodPressure, dtype: int64

In [42]: plt.hist(Positive['SkinThickness'],histtype='stepfilled',bins=20)

Out[42]: (array([88., 1., 4., 10., 18., 30., 41., 34., 23., 15., 1., 1., 1.,
0., 0., 0., 0., 0., 0., 1.]),
array([ 0. , 4.95, 9.9 , 14.85, 19.8 , 24.75, 29.7 , 34.65, 39.6 ,
44.55, 49.5 , 54.45, 59.4 , 64.35, 69.3 , 74.25, 79.2 , 84.15,
89.1 , 94.05, 99. ]),
[<matplotlib.patches.Polygon at 0x1180d654e50>])

In [43]: Positive['SkinThickness'].value_counts().head()

Out[43]: 0 88
32 14
33 9
30 9
39 8
Name: SkinThickness, dtype: int64

In [44]: plt.hist(Positive['Insulin'],histtype='stepfilled',bins=20)

Out[44]: (array([141., 6., 23., 33., 24., 12., 7., 7., 2., 1., 1.,
5., 3., 1., 1., 0., 0., 0., 0., 1.]),
array([ 0. , 42.3, 84.6, 126.9, 169.2, 211.5, 253.8, 296.1, 338.4,
380.7, 423. , 465.3, 507.6, 549.9, 592.2, 634.5, 676.8, 719.1,
761.4, 803.7, 846. ]),
[<matplotlib.patches.Polygon at 0x1180d43b850>])

In [46]: Positive['Insulin'].value_counts().head()

Out[46]: 0 138
130 6
180 4
 156 3
175 3
Name: Insulin, dtype: int64

In [47]: BloodPressure = Positive['BloodPressure']

Glucose = Positive['Glucose']
SkinThickness = Positive['SkinThickness']
Insulin = Positive['Insulin']
BMI = Positive['BMI']

In [48]: plt.scatter(BloodPressure, Glucose, color=['b'])

plt.xlabel('BloodPressure')
plt.ylabel('Glucose')
plt.title('BloodPressure & Glucose')
plt.show()

In [52]: g =sns.scatterplot(x="Glucose",y="BloodPressure",
hue="Outcome",
data=df);

In [53]: B =sns.scatterplot(x= "BMI" ,y= "Insulin",

hue="Outcome",
data=df);
In [54]: S =sns.scatterplot(x= "SkinThickness" ,y= "Insulin",
hue="Outcome",
data=df);

In [55]: df.corr()

Out[55]: Pregnancies Glucose BloodPressure SkinThickness Insulin BMI DiabetesPedi

Pregnancies 1.000000 0.129459 0.141282 -0.081672 -0.073535 0.017683

Glucose 0.129459 1.000000 0.152590 0.057328 0.331357 0.221071

BloodPressure 0.141282 0.152590 1.000000 0.207371 0.088933 0.281805

SkinThickness -0.081672 0.057328 0.207371 1.000000 0.436783 0.392573

Insulin -0.073535 0.331357 0.088933 0.436783 1.000000 0.197859

BMI 0.017683 0.221071 0.281805 0.392573 0.197859 1.000000

DiabetesPedigreeFunction -0.033523 0.137337 0.041265 0.183928 0.185071 0.140647

Age 0.544341 0.263514 0.239528 -0.113970 -0.042163 0.036242

Outcome 0.221898 0.466581 0.065068 0.074752 0.130548 0.292695

In [56]: sns.heatmap(df.corr())

Out[56]: <AxesSubplot:>
In [57]: plt.subplots(figsize=(8,8))
sns.heatmap(df.corr(),annot=True,cmap='viridis')

Out[57]: <AxesSubplot:>

In [58]: plt.subplots(figsize=(8,8))
sns.heatmap(df.corr(),annot=True)
Out[58]: <AxesSubplot:>

In [59]: df.head(5)

Out[59]: Pregnancies Glucose BloodPressure SkinThickness Insulin BMI DiabetesPedigreeFunction Age Outcome

0 6 148 72 35 0 33.6 0.627 50 1

1 1 85 66 29 0 26.6 0.351 31 0

2 8 183 64 0 0 23.3 0.672 32 1

3 1 89 66 23 94 28.1 0.167 21 0

4 0 137 40 35 168 43.1 2.288 33 1

In [60]: features = df.iloc[:,[0,1,2,3,4,5,6,7]].values

label = df.iloc[:,8].values

In [61]: from sklearn.model_selection import train_test_split

X_train,X_test,y_train,y_test = train_test_split(features,label,test_size=0.2,random_state =10)

In [62]: from sklearn.linear_model import LogisticRegression

model = LogisticRegression()
model.fit(X_train,y_train)

Out[62]: LogisticRegression()

In [63]: print(model.score(X_train,y_train))
print(model.score(X_test,y_test))
 0.7719869706840391
0.7662337662337663

In [64]: from sklearn.metrics import confusion_matrix

cm = confusion_matrix(label,model.predict(features))
cm

Out[64]: array([[446, 54],

[122, 146]], dtype=int64)

In [65]: from sklearn.metrics import classification_report

print(classification_report(label,model.predict(features)))

precision recall f1-score support

0 0.79 0.89 0.84 500

1 0.73 0.54 0.62 268

accuracy 0.77 768

macro avg 0.76 0.72 0.73 768
weighted avg 0.77 0.77 0.76 768

In [66]: from sklearn.metrics import roc_curve

from sklearn.metrics import roc_auc_score
# predict probabilities
probs = model.predict_proba(features)
# keep probabilities for the positive outcome only
probs = probs[:, 1]
# calculate AUC
auc = roc_auc_score(label, probs)
print('AUC: %.3f' % auc)
# calculate roc curve
fpr, tpr, thresholds = roc_curve(label, probs)
# plot no skill
plt.plot([0, 1], [0, 1], linestyle='--')
# plot the roc curve for the model
plt.plot(fpr, tpr, marker='.')

AUC: 0.837
Out[66]: [<matplotlib.lines.Line2D at 0x1180f5e6340>]

In [67]: from sklearn.tree import DecisionTreeClassifier

model3 = DecisionTreeClassifier(max_depth=5)
model3.fit(X_train,y_train)

Out[67]: DecisionTreeClassifier(max_depth=5)

In [68]: model3.score(X_train,y_train)

Out[68]: 0.8289902280130294

In [69]: model3.score(X_test,y_test)
Out[69]: 0.7597402597402597

In [70]: from sklearn.ensemble import RandomForestClassifier

model4 = RandomForestClassifier(n_estimators=11)
model4.fit(X_train,y_train)

Out[70]: RandomForestClassifier(n_estimators=11)

In [71]: model4.score(X_train,y_train)

Out[71]: 0.988599348534202

In [72]: model4.score(X_test,y_test)

Out[72]: 0.7467532467532467

In [73]: from sklearn.svm import SVC

model5 = SVC(kernel='rbf',
gamma='auto')
model5.fit(X_train,y_train)

Out[73]: SVC(gamma='auto')

In [74]: model5.score(X_test,y_test)

Out[74]: 0.6168831168831169

In [75]: from sklearn.neighbors import KNeighborsClassifier

model2 = KNeighborsClassifier(n_neighbors=7,
metric='minkowski',
p = 2)
model2.fit(X_train,y_train)

Out[75]: KNeighborsClassifier(n_neighbors=7)

In [76]: from sklearn.metrics import roc_curve

from sklearn.metrics import roc_auc_score

# predict probabilities
probs = model2.predict_proba(features)
# keep probabilities for the positive outcome only
probs = probs[:, 1]
# calculate AUC
auc = roc_auc_score(label, probs)
print('AUC: %.3f' % auc)
# calculate roc curve
fpr, tpr, thresholds = roc_curve(label, probs)
print("True Positive Rate - {}, False Positive Rate - {} Thresholds - {}".format(tpr,fpr,thresh
# plot no skill
plt.plot([0, 1], [0, 1], linestyle='--')
# plot the roc curve for the model
plt.plot(fpr, tpr, marker='.')
plt.xlabel("False Positive Rate")
plt.ylabel("True Positive Rate")

AUC: 0.836
True Positive Rate - [0. 0.06716418 0.23880597 0.44776119 0.60074627 0.75373134
0.88059701 0.98507463 1. ], False Positive Rate - [0. 0. 0.02 0.056 0.12 0.248
0.428 0.668 1. ] Thresholds - [2. 1. 0.85714286 0.71428571 0.57142857 0.42857
143
0.28571429 0.14285714 0. ]
Out[76]: Text(0, 0.5, 'True Positive Rate')
In [77]: from sklearn.metrics import precision_recall_curve
from sklearn.metrics import f1_score
from sklearn.metrics import auc
from sklearn.metrics import average_precision_score
# predict probabilities
probs = model.predict_proba(features)
# keep probabilities for the positive outcome only
probs = probs[:, 1]
# predict class values
yhat = model.predict(features)
# calculate precision-recall curve
precision, recall, thresholds = precision_recall_curve(label, probs)
# calculate F1 score
f1 = f1_score(label, yhat)
# calculate precision-recall AUC
auc = auc(recall, precision)
# calculate average precision score
ap = average_precision_score(label, probs)
print('f1=%.3f auc=%.3f ap=%.3f' % (f1, auc, ap))
# plot no skill
plt.plot([0, 1], [0.5, 0.5], linestyle='--')
# plot the precision-recall curve for the model
plt.plot(recall, precision, marker='.')

f1=0.624 auc=0.726 ap=0.727

Out[77]: [<matplotlib.lines.Line2D at 0x1180f892490>]

In [78]: from sklearn.metrics import precision_recall_curve

from sklearn.metrics import f1_score
from sklearn.metrics import auc
from sklearn.metrics import average_precision_score
# predict probabilities
probs = model2.predict_proba(features)
# keep probabilities for the positive outcome only
probs = probs[:, 1]
 # predict class values
yhat = model2.predict(features)
# calculate precision-recall curve
precision, recall, thresholds = precision_recall_curve(label, probs)
# calculate F1 score
f1 = f1_score(label, yhat)
# calculate precision-recall AUC
auc = auc(recall, precision)
# calculate average precision score
ap = average_precision_score(label, probs)
print('f1=%.3f auc=%.3f ap=%.3f' % (f1, auc, ap))
# plot no skill
plt.plot([0, 1], [0.5, 0.5], linestyle='--')
# plot the precision-recall curve for the model
plt plot(recall precision marker=' ')
f1=0.658 auc=0.752 ap=0.709
Out[78]: [<matplotlib.lines.Line2D at 0x1180f8f35b0>]

In [79]: from sklearn.metrics import precision_recall_curve

from sklearn.metrics import f1_score
from sklearn.metrics import auc
from sklearn.metrics import average_precision_score
# predict probabilities
probs = model3.predict_proba(features)
# keep probabilities for the positive outcome only
probs = probs[:, 1]
# predict class values
yhat = model3.predict(features)
# calculate precision-recall curve
precision, recall, thresholds = precision_recall_curve(label, probs)
# calculate F1 score
f1 = f1_score(label, yhat)
# calculate precision-recall AUC
auc = auc(recall, precision)
# calculate average precision score
ap = average_precision_score(label, probs)
print('f1=%.3f auc=%.3f ap=%.3f' % (f1, auc, ap))
# plot no skill
plt.plot([0, 1], [0.5, 0.5], linestyle='--')
# plot the precision-recall curve for the model
plt.plot(recall, precision, marker='.')

f1=0.710 auc=0.797 ap=0.758

Out[79]: [<matplotlib.lines.Line2D at 0x1180f9506d0>]
In [80]: from sklearn.metrics import precision_recall_curve
from sklearn.metrics import f1_score
from sklearn.metrics import auc
from sklearn.metrics import average_precision_score
# predict probabilities
probs = model4.predict_proba(features)
# keep probabilities for the positive outcome only
probs = probs[:, 1]
# predict class values
yhat = model4.predict(features)
# calculate precision-recall curve
precision, recall, thresholds = precision_recall_curve(label, probs)
# calculate F1 score
f1 = f1_score(label, yhat)
# calculate precision-recall AUC
auc = auc(recall, precision)
# calculate average precision score
ap = average_precision_score(label, probs)
print('f1=%.3f auc=%.3f ap=%.3f' % (f1, auc, ap))
# plot no skill
plt.plot([0, 1], [0.5, 0.5], linestyle='--')
# plot the precision-recall curve for the model
plt.plot(recall, precision, marker='.')

f1=0.910 auc=0.969 ap=0.961

Out[80]: [<matplotlib.lines.Line2D at 0x1180f9ac820>]