DATA SCIENCE PROJECT

Manish Dwari ,18047

Indian Institute of Science Education and Research (IISER) Berhampur

SUB: Introduction to Data Science (IDC 301)

TOPIC: Breast Cancer Wisconsin (Diagnostics) data Analysis and prediction

IMPORTING FUNCTIONS

In [1]: import pandas as pd

import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt

In [2]: from sklearn.tree import DecisionTreeClassifier

from sklearn.metrics import confusion_matrix, classification_report,accuracy_score
from sklearn.preprocessing import StandardScaler
from sklearn import linear_model
from sklearn.model_selection import train_test_split
from sklearn import tree
from sklearn import svm
from sklearn.feature_selection import SelectKBest
from sklearn.feature_selection import chi2

LOADING AND VISUALISING DATA

In [3]: data=pd.read_csv('data1.csv')
data.tail(10)

Out[3]: concave
id diagnosis radius_mean texture_mean perimeter_mean area_mean smoothness_mean compactness_mean concavity_mean ... texture_worst perimeter_wor
points_mean

559 925291 B 11.51 23.93 74.52 403.5 0.09261 0.10210 0.11120 0.04105 ... 37.16 82.2

560 925292 B 14.05 27.15 91.38 600.4 0.09929 0.11260 0.04462 0.04304 ... 33.17 100.2

561 925311 B 11.20 29.37 70.67 386.0 0.07449 0.03558 0.00000 0.00000 ... 38.30 75.1

562 925622 M 15.22 30.62 103.40 716.9 0.10480 0.20870 0.25500 0.09429 ... 42.79 128.7

563 926125 M 20.92 25.09 143.00 1347.0 0.10990 0.22360 0.31740 0.14740 ... 29.41 179.1

564 926424 M 21.56 22.39 142.00 1479.0 0.11100 0.11590 0.24390 0.13890 ... 26.40 166.1

565 926682 M 20.13 28.25 131.20 1261.0 0.09780 0.10340 0.14400 0.09791 ... 38.25 155.0

566 926954 M 16.60 28.08 108.30 858.1 0.08455 0.10230 0.09251 0.05302 ... 34.12 126.7

567 927241 M 20.60 29.33 140.10 1265.0 0.11780 0.27700 0.35140 0.15200 ... 39.42 184.6

568 92751 B 7.76 24.54 47.92 181.0 0.05263 0.04362 0.00000 0.00000 ... 30.37 59.1

10 rows × 33 columns

In [4]: data.shape

Out[4]: (569, 33)

In [5]: data['diagnosis'].tail()

Out[5]: 564 M
565 M
566 M
567 M
568 B
Name: diagnosis, dtype: object

In [6]: data.describe()

Out[6]: concave
id radius_mean texture_mean perimeter_mean area_mean smoothness_mean compactness_mean concavity_mean symmetry_mean ... texture_worst
points_mean

count 5.690000e+02 569.000000 569.000000 569.000000 569.000000 569.000000 569.000000 569.000000 569.000000 569.000000 ... 569.000000

mean 3.037183e+07 14.127292 19.289649 91.969033 654.889104 0.096360 0.104341 0.088799 0.048919 0.181162 ... 25.677223

std 1.250206e+08 3.524049 4.301036 24.298981 351.914129 0.014064 0.052813 0.079720 0.038803 0.027414 ... 6.146258

min 8.670000e+03 6.981000 9.710000 43.790000 143.500000 0.052630 0.019380 0.000000 0.000000 0.106000 ... 12.020000

25% 8.692180e+05 11.700000 16.170000 75.170000 420.300000 0.086370 0.064920 0.029560 0.020310 0.161900 ... 21.080000

50% 9.060240e+05 13.370000 18.840000 86.240000 551.100000 0.095870 0.092630 0.061540 0.033500 0.179200 ... 25.410000

75% 8.813129e+06 15.780000 21.800000 104.100000 782.700000 0.105300 0.130400 0.130700 0.074000 0.195700 ... 29.720000

max 9.113205e+08 28.110000 39.280000 188.500000 2501.000000 0.163400 0.345400 0.426800 0.201200 0.304000 ... 49.540000

8 rows × 32 columns

In [7]: print(data['diagnosis'].value_counts())

B 357
M 212
Name: diagnosis, dtype: int64
CHECKING FOR MISSING/NULL VALUES

In [8]: print(data.isnull().isnull().sum())

id 0
diagnosis 0
radius_mean 0
texture_mean 0
perimeter_mean 0
area_mean 0
smoothness_mean 0
compactness_mean 0
concavity_mean 0
concave points_mean 0
symmetry_mean 0
fractal_dimension_mean 0
radius_se 0
texture_se 0
perimeter_se 0
area_se 0
smoothness_se 0
compactness_se 0
concavity_se 0
concave points_se 0
symmetry_se 0
fractal_dimension_se 0
radius_worst 0
texture_worst 0
perimeter_worst 0
area_worst 0
smoothness_worst 0
compactness_worst 0
concavity_worst 0
concave points_worst 0
symmetry_worst 0
fractal_dimension_worst 0
Unnamed: 32 0
dtype: int64

In [9]: data.drop(['id','Unnamed: 32'],axis=1,inplace=True)

In [10]: data.info()

<class 'pandas.core.frame.DataFrame'>
RangeIndex: 569 entries, 0 to 568
Data columns (total 31 columns):
# Column Non-Null Count Dtype
--- ------ -------------- -----
0 diagnosis 569 non-null object
1 radius_mean 569 non-null float64
2 texture_mean 569 non-null float64
3 perimeter_mean 569 non-null float64
4 area_mean 569 non-null float64
5 smoothness_mean 569 non-null float64
6 compactness_mean 569 non-null float64
7 concavity_mean 569 non-null float64
8 concave points_mean 569 non-null float64
9 symmetry_mean 569 non-null float64
10 fractal_dimension_mean 569 non-null float64
11 radius_se 569 non-null float64
12 texture_se 569 non-null float64
13 perimeter_se 569 non-null float64
14 area_se 569 non-null float64
15 smoothness_se 569 non-null float64
16 compactness_se 569 non-null float64
17 concavity_se 569 non-null float64
18 concave points_se 569 non-null float64
19 symmetry_se 569 non-null float64
20 fractal_dimension_se 569 non-null float64
21 radius_worst 569 non-null float64
22 texture_worst 569 non-null float64
23 perimeter_worst 569 non-null float64
24 area_worst 569 non-null float64
25 smoothness_worst 569 non-null float64
26 compactness_worst 569 non-null float64
27 concavity_worst 569 non-null float64
28 concave points_worst 569 non-null float64
29 symmetry_worst 569 non-null float64
30 fractal_dimension_worst 569 non-null float64
dtypes: float64(30), object(1)
memory usage: 137.9+ KB

In [11]: data.columns

Out[11]: Index(['diagnosis', 'radius_mean', 'texture_mean', 'perimeter_mean',

'area_mean', 'smoothness_mean', 'compactness_mean', 'concavity_mean',
'concave points_mean', 'symmetry_mean', 'fractal_dimension_mean',
'radius_se', 'texture_se', 'perimeter_se', 'area_se', 'smoothness_se',
'compactness_se', 'concavity_se', 'concave points_se', 'symmetry_se',
'fractal_dimension_se', 'radius_worst', 'texture_worst',
'perimeter_worst', 'area_worst', 'smoothness_worst',
'compactness_worst', 'concavity_worst', 'concave points_worst',
'symmetry_worst', 'fractal_dimension_worst'],
dtype='object')

DATA VISUALIZATION AND EXPLORATION GRAPHICALLY

In [12]: sns.countplot(data['diagnosis'])

C:\Users\lenovo\anaconda3\lib\site-packages\seaborn\_decorators.py:36: FutureWarning: Pass the following variable as a keyword arg: x. From version
0.12, the only valid positional argument will be `data`, and passing other arguments without an explicit keyword will result in an error or misinte
rpretation.
warnings.warn(
Out[12]: <AxesSubplot:xlabel='diagnosis', ylabel='count'>

In [13]: cor=data.corr() #checking for correlation

cor

Out[13]: concave
radius_mean texture_mean perimeter_mean area_mean smoothness_mean compactness_mean concavity_mean symmetry_mean fractal_dimensio
points_mean

radius_mean 1.000000 0.323782 0.997855 0.987357 0.170581 0.506124 0.676764 0.822529 0.147741 -

texture_mean 0.323782 1.000000 0.329533 0.321086 -0.023389 0.236702 0.302418 0.293464 0.071401 -

perimeter_mean 0.997855 0.329533 1.000000 0.986507 0.207278 0.556936 0.716136 0.850977 0.183027 -

area_mean 0.987357 0.321086 0.986507 1.000000 0.177028 0.498502 0.685983 0.823269 0.151293 -

smoothness_mean 0.170581 -0.023389 0.207278 0.177028 1.000000 0.659123 0.521984 0.553695 0.557775

compactness_mean 0.506124 0.236702 0.556936 0.498502 0.659123 1.000000 0.883121 0.831135 0.602641

concavity_mean 0.676764 0.302418 0.716136 0.685983 0.521984 0.883121 1.000000 0.921391 0.500667

concave points_mean 0.822529 0.293464 0.850977 0.823269 0.553695 0.831135 0.921391 1.000000 0.462497

symmetry_mean 0.147741 0.071401 0.183027 0.151293 0.557775 0.602641 0.500667 0.462497 1.000000

fractal_dimension_mean -0.311631 -0.076437 -0.261477 -0.283110 0.584792 0.565369 0.336783 0.166917 0.479921

radius_se 0.679090 0.275869 0.691765 0.732562 0.301467 0.497473 0.631925 0.698050 0.303379

texture_se -0.097317 0.386358 -0.086761 -0.066280 0.068406 0.046205 0.076218 0.021480 0.128053

perimeter_se 0.674172 0.281673 0.693135 0.726628 0.296092 0.548905 0.660391 0.710650 0.313893

area_se 0.735864 0.259845 0.744983 0.800086 0.246552 0.455653 0.617427 0.690299 0.223970 -

smoothness_se -0.222600 0.006614 -0.202694 -0.166777 0.332375 0.135299 0.098564 0.027653 0.187321

compactness_se 0.206000 0.191975 0.250744 0.212583 0.318943 0.738722 0.670279 0.490424 0.421659

concavity_se 0.194204 0.143293 0.228082 0.207660 0.248396 0.570517 0.691270 0.439167 0.342627

concave points_se 0.376169 0.163851 0.407217 0.372320 0.380676 0.642262 0.683260 0.615634 0.393298

symmetry_se -0.104321 0.009127 -0.081629 -0.072497 0.200774 0.229977 0.178009 0.095351 0.449137

fractal_dimension_se -0.042641 0.054458 -0.005523 -0.019887 0.283607 0.507318 0.449301 0.257584 0.331786

radius_worst 0.969539 0.352573 0.969476 0.962746 0.213120 0.535315 0.688236 0.830318 0.185728 -

texture_worst 0.297008 0.912045 0.303038 0.287489 0.036072 0.248133 0.299879 0.292752 0.090651 -

perimeter_worst 0.965137 0.358040 0.970387 0.959120 0.238853 0.590210 0.729565 0.855923 0.219169 -

area_worst 0.941082 0.343546 0.941550 0.959213 0.206718 0.509604 0.675987 0.809630 0.177193 -

smoothness_worst 0.119616 0.077503 0.150549 0.123523 0.805324 0.565541 0.448822 0.452753 0.426675

compactness_worst 0.413463 0.277830 0.455774 0.390410 0.472468 0.865809 0.754968 0.667454 0.473200

concavity_worst 0.526911 0.301025 0.563879 0.512606 0.434926 0.816275 0.884103 0.752399 0.433721

concave points_worst 0.744214 0.295316 0.771241 0.722017 0.503053 0.815573 0.861323 0.910155 0.430297

symmetry_worst 0.163953 0.105008 0.189115 0.143570 0.394309 0.510223 0.409464 0.375744 0.699826

fractal_dimension_worst 0.007066 0.119205 0.051019 0.003738 0.499316 0.687382 0.514930 0.368661 0.438413

30 rows × 30 columns

In [14]: plt.figure(figsize=(20,10))
sns.heatmap(cor,annot=True) #STUDYING CORRELATION USING HEATMAP

Out[14]: <AxesSubplot:>

In [15]: dt=data.drop(data.iloc[:,11:32],axis=1) #dropping some features of the data for better visualisation
dt.columns

Out[15]: Index(['diagnosis', 'radius_mean', 'texture_mean', 'perimeter_mean',

'area_mean', 'smoothness_mean', 'compactness_mean', 'concavity_mean',
'concave points_mean', 'symmetry_mean', 'fractal_dimension_mean'],
dtype='object')

In [16]: sns.pairplot(dt, hue='diagnosis')

Out[16]: <seaborn.axisgrid.PairGrid at 0x249e28ad3a0>

In [17]: for i in ('radius_mean', 'texture_mean', 'perimeter_mean',

'area_mean', 'smoothness_mean', 'compactness_mean', 'concavity_mean',
'concave points_mean', 'symmetry_mean', 'fractal_dimension_mean'):
dt[i][dt['diagnosis']=='M'].plot.kde(title=i,c='r')
dt[i][dt['diagnosis']=='B'].plot.kde(title=i,c='g')
plt.show()

In [18]: for i in ('radius_mean', 'texture_mean', 'perimeter_mean',

'area_mean', 'smoothness_mean', 'compactness_mean', 'concavity_mean',
'concave points_mean', 'symmetry_mean', 'fractal_dimension_mean'):
dt[i].plot.kde(title=i)
plt.show()

In [19]: sns.heatmap(dt.corr(),annot=True)

Out[19]: <AxesSubplot:>

PREPROCESSING AND PRIDICTION

In [20]: data.head()

Out[20]: concave
diagnosis radius_mean texture_mean perimeter_mean area_mean smoothness_mean compactness_mean concavity_mean symmetry_mean ... radius_worst texture_
points_mean

0 M 17.99 10.38 122.80 1001.0 0.11840 0.27760 0.3001 0.14710 0.2419 ... 25.38

1 M 20.57 17.77 132.90 1326.0 0.08474 0.07864 0.0869 0.07017 0.1812 ... 24.99

2 M 19.69 21.25 130.00 1203.0 0.10960 0.15990 0.1974 0.12790 0.2069 ... 23.57

3 M 11.42 20.38 77.58 386.1 0.14250 0.28390 0.2414 0.10520 0.2597 ... 14.91

4 M 20.29 14.34 135.10 1297.0 0.10030 0.13280 0.1980 0.10430 0.1809 ... 22.54

5 rows × 31 columns

FEATURE SELECTION TO AVOID CURSE OF DIMENTIONALITY

In [21]: x=data.drop('diagnosis',axis=1)
y=data['diagnosis']

In [22]: bestfeatures = SelectKBest(score_func=chi2, k=16)

fit= bestfeatures.fit(x,y)
dfscores = pd.DataFrame(fit.scores_)
dfcolumns = pd.DataFrame(x.columns)

In [23]: fscores = pd.concat([dfcolumns,dfscores],axis=1)

fscores.columns = ['feat','Score']

In [24]: fscores

Out[24]: feat Score

0 radius_mean 266.104917

1 texture_mean 93.897508

2 perimeter_mean 2011.102864

3 area_mean 53991.655924

4 smoothness_mean 0.149899

5 compactness_mean 5.403075

6 concavity_mean 19.712354

7 concave points_mean 10.544035

8 symmetry_mean 0.257380

9 fractal_dimension_mean 0.000074

10 radius_se 34.675247

11 texture_se 0.009794

12 perimeter_se 250.571896

13 area_se 8758.504705

14 smoothness_se 0.003266

15 compactness_se 0.613785

16 concavity_se 1.044718

17 concave points_se 0.305232

18 symmetry_se 0.000080

19 fractal_dimension_se 0.006371

20 radius_worst 491.689157

21 texture_worst 174.449400

22 perimeter_worst 3665.035416

23 area_worst 112598.431564

24 smoothness_worst 0.397366

25 compactness_worst 19.314922

26 concavity_worst 39.516915

27 concave points_worst 13.485419

28 symmetry_worst 1.298861

29 fractal_dimension_worst 0.231522

In [25]: fscores.plot(kind='barh')
plt.show()

In [26]: print(fscores.nlargest(16,'Score'))

feat Score
23 area_worst 112598.431564
3 area_mean 53991.655924
13 area_se 8758.504705
22 perimeter_worst 3665.035416
2 perimeter_mean 2011.102864
20 radius_worst 491.689157
0 radius_mean 266.104917
12 perimeter_se 250.571896
21 texture_worst 174.449400
1 texture_mean 93.897508
26 concavity_worst 39.516915
10 radius_se 34.675247
6 concavity_mean 19.712354
25 compactness_worst 19.314922
27 concave points_worst 13.485419
7 concave points_mean 10.544035

In [27]: dp=data.drop(['smoothness_mean', 'compactness_mean', 'symmetry_mean',

'fractal_dimension_mean', 'texture_se', 'smoothness_se',
'compactness_se', 'concavity_se', 'concave points_se', 'symmetry_se',
'fractal_dimension_se', 'smoothness_worst', 'symmetry_worst',
'fractal_dimension_worst'],axis=1)
dp.columns

Out[27]: Index(['diagnosis', 'radius_mean', 'texture_mean', 'perimeter_mean',

'area_mean', 'concavity_mean', 'concave points_mean', 'radius_se',
'perimeter_se', 'area_se', 'radius_worst', 'texture_worst',
'perimeter_worst', 'area_worst', 'compactness_worst', 'concavity_worst',
'concave points_worst'],
dtype='object')

In [28]: dp.shape

Out[28]: (569, 17)

SPLITING THE DATA INTO TEST AND TRAIN

In [29]: X=dp.drop('diagnosis',axis=1)
Y=dp['diagnosis']
Y=Y.map({'B':0,'M':1})
Y.tail()

Out[29]: 564 1
565 1
566 1
567 1
568 0
Name: diagnosis, dtype: int64

In [30]: X.shape

Out[30]: (569, 16)

In [31]: X_train,X_test,Y_train,Y_test=train_test_split(X,Y,test_size=0.2,random_state=0)
print(X_train.var())

radius_mean 12.498873
texture_mean 17.296973
perimeter_mean 591.122540
area_mean 128283.011726
concavity_mean 0.006053
concave points_mean 0.001490
radius_se 0.080867
perimeter_se 4.152441
area_se 2278.193100
radius_worst 23.917513
texture_worst 37.217703
perimeter_worst 1147.121834
area_worst 343859.863025
compactness_worst 0.023442
concavity_worst 0.039855
concave points_worst 0.004267
dtype: float64

In [32]: s=StandardScaler() #fitting the data to normal distribution or standadizing for results
X_train=s.fit_transform(X_train)
X_test=s.transform(X_test)

APPLYING DECISION TREE CLASSIFIER MODEL

In [33]: mod=DecisionTreeClassifier()
mod.fit(X_train,Y_train)
p=mod.predict(X_test)

In [34]: print(classification_report(Y_test,p))

precision recall f1-score support

0 0.97 0.96 0.96 67

1 0.94 0.96 0.95 47

accuracy 0.96 114

macro avg 0.95 0.96 0.95 114
weighted avg 0.96 0.96 0.96 114

In [35]: cm=confusion_matrix(Y_test,p)
sns.heatmap(cm,annot=True)

Out[35]: <AxesSubplot:>

In [36]: print(accuracy_score(Y_test,p))

0.956140350877193

In [63]: import graphviz

from IPython.display import Image

In [38]: dt = tree.export_graphviz(mod,out_file=None,feature_names=X.columns,
class_names=data.columns[1],filled=True,rounded=True,special_characters=True)
g = graphviz.Source(dt)
g #PLOTING THE DESICION TREE

concave points_worst ≤ 0.428

Out[38]: gini = 0.462
samples = 455
value = [290, 165]
class = r
True False

area_worst ≤ 0.13 area_worst ≤ -0.259

gini = 0.146 gini = 0.134
samples = 303 samples = 152
value = [279, 24] value = [11, 141]
class = r class = a

perimeter_worst ≤ 0.021 texture_mean ≤ -0.158 concave points_worst ≤ 1.016 radius_se ≤ -0.789

gini = 0.073 gini = 0.231 gini = 0.49 gini = 0.043
samples = 288 samples = 15 samples = 14 samples = 138
value = [277, 11] value = [2, 13] value = [8, 6] value = [3, 135]
class = r class = a class = r class = a

area_se ≤ 1.075 perimeter_mean ≤ 0.004 area_se ≤ 0.466 texture_worst ≤ 0.94 concavity_worst ≤ -0.321
gini = 0.0 gini = 0.0 gini = 0.0
gini = 0.036 gini = 0.432 gini = 0.444 gini = 0.198 gini = 0.029
samples = 12 samples = 5 samples = 1
samples = 269 samples = 19 samples = 3 samples = 9 samples = 137
value = [0, 12] value = [0, 5] value = [1, 0]
value = [264, 5] value = [13, 6] value = [2, 1] value = [8, 1] value = [2, 135]
class = a class = a class = r
class = r class = r class = r class = r class = a

concavity_mean ≤ 0.692 perimeter_se ≤ 0.0 texture_mean ≤ -0.911

gini = 0.0 gini = 0.0 gini = 0.0 gini = 0.0 gini = 0.0 gini = 0.0 gini = 0.0
gini = 0.029 gini = 0.231 gini = 0.015
samples = 1 samples = 4 samples = 2 samples = 1 samples = 8 samples = 1 samples = 1
samples = 268 samples = 15 samples = 136
value = [0, 1] value = [0, 4] value = [2, 0] value = [0, 1] value = [8, 0] value = [0, 1] value = [1, 0]
value = [264, 4] value = [13, 2] value = [1, 135]
class = a class = a class = r class = a class = r class = a class = r
class = r class = r class = a

area_se ≤ 0.182 concavity_worst ≤ 0.948 texture_worst ≤ -0.535 area_worst ≤ -0.012

gini = 0.0 gini = 0.0
gini = 0.022 gini = 0.444 gini = 0.444 gini = 0.32
samples = 12 samples = 131
samples = 265 samples = 3 samples = 3 samples = 5
value = [12, 0] value = [0, 131]
value = [262, 3] value = [2, 1] value = [1, 2] value = [1, 4]
class = r class = a
class = r class = r class = a class = a

texture_worst ≤ 0.756 radius_mean ≤ -0.523

gini = 0.0 gini = 0.0 gini = 0.0 gini = 0.0 gini = 0.0 gini = 0.0
gini = 0.015 gini = 0.444
samples = 1 samples = 2 samples = 1 samples = 2 samples = 1 samples = 4
samples = 262 samples = 3
value = [0, 1] value = [2, 0] value = [1, 0] value = [0, 2] value = [1, 0] value = [0, 4]
value = [260, 2] value = [2, 1]
class = a class = r class = r class = a class = r class = a
class = r class = r

texture_worst ≤ 0.782
gini = 0.0 gini = 0.0 gini = 0.0
gini = 0.117
samples = 230 samples = 1 samples = 2
samples = 32
value = [230, 0] value = [0, 1] value = [2, 0]
value = [30, 2]
class = r class = a class = r
class = r

radius_worst ≤ -0.374
gini = 0.0
gini = 0.062
samples = 1
samples = 31
value = [0, 1]
value = [30, 1]
class = a
class = r

perimeter_worst ≤ -0.374
gini = 0.0
gini = 0.245
samples = 24
samples = 7
value = [24, 0]
value = [6, 1]
class = r
class = r

gini = 0.0 gini = 0.0

samples = 1 samples = 6
value = [0, 1] value = [6, 0]
class = a class = r

In [67]: g.render('Decision Tree')

Out[67]: 'Decision Tree.pdf'

APPLYING LINEAR REGRESSION MODEL

In [39]: mod2=linear_model.LogisticRegression()
mod2.fit(X_train,Y_train)
pe=mod2.predict(X_test)
pe=np.array(mod2.predict(X_test))

In [40]: print(classification_report(Y_test,pe))

precision recall f1-score support

0 0.97 0.96 0.96 67

1 0.94 0.96 0.95 47

accuracy 0.96 114

macro avg 0.95 0.96 0.95 114
weighted avg 0.96 0.96 0.96 114

In [41]: cm1=confusion_matrix(Y_test,pe)
sns.heatmap(cm1,annot=True)

Out[41]: <AxesSubplot:>

In [42]: print(accuracy_score(Y_test,pe))

0.956140350877193
APPLYING SUPPORT VECTOR CLASSIFIER MODEL

In [43]: mod3=svm.SVC()
mod3.fit(X_train,Y_train)
ped=mod3.predict(X_test)

In [44]: print(classification_report(Y_test,ped))

precision recall f1-score support

0 0.98 0.96 0.97 67

1 0.94 0.98 0.96 47

accuracy 0.96 114

macro avg 0.96 0.97 0.96 114
weighted avg 0.97 0.96 0.97 114

In [45]: cm2=confusion_matrix(Y_test,ped)
sns.heatmap(cm2,annot=True)

Out[45]: <AxesSubplot:>

In [46]: print(accuracy_score(Y_test,ped))

0.9649122807017544

PRIDICTION WITH FULL DATA

In [47]: X=data.drop('diagnosis',axis=1)
Y=data['diagnosis']
Y=Y.map({'B':0,'M':1})
Y.tail()

Out[47]: 564 1
565 1
566 1
567 1
568 0
Name: diagnosis, dtype: int64

In [48]: X_train,X_test,Y_train,Y_test=train_test_split(X,Y,test_size=0.2,random_state=0)
print(X_train.var())

radius_mean 12.498873
texture_mean 17.296973
perimeter_mean 591.122540
area_mean 128283.011726
smoothness_mean 0.000190
compactness_mean 0.002549
concavity_mean 0.006053
concave points_mean 0.001490
symmetry_mean 0.000751
fractal_dimension_mean 0.000046
radius_se 0.080867
texture_se 0.293722
perimeter_se 4.152441
area_se 2278.193100
smoothness_se 0.000008
compactness_se 0.000307
concavity_se 0.000968
concave points_se 0.000035
symmetry_se 0.000067
fractal_dimension_se 0.000007
radius_worst 23.917513
texture_worst 37.217703
perimeter_worst 1147.121834
area_worst 343859.863025
smoothness_worst 0.000512
compactness_worst 0.023442
concavity_worst 0.039855
concave points_worst 0.004267
symmetry_worst 0.003968
fractal_dimension_worst 0.000317
dtype: float64

In [49]: s=StandardScaler()
X_train=s.fit_transform(X_train)
X_test=s.transform(X_test)

APPLYING LINEAR REGRESSION

In [50]: mod2=linear_model.LogisticRegression()
mod2.fit(X_train,Y_train)
pe=mod2.predict(X_test)
pe=np.array(mod2.predict(X_test))
Y=np.array(Y_test)

In [51]: print(accuracy_score(Y_test,pe))

0.9649122807017544

In [52]: print(classification_report(Y_test,pe))

precision recall f1-score support

0 0.97 0.97 0.97 67

1 0.96 0.96 0.96 47

accuracy 0.96 114

macro avg 0.96 0.96 0.96 114
weighted avg 0.96 0.96 0.96 114

In [53]: c1=confusion_matrix(Y_test,pe)
sns.heatmap(c1,annot=True)

Out[53]: <AxesSubplot:>

APPLYING SUPPORT VECTOR CLASSIFIER

In [54]: mod3=svm.SVC()
mod3.fit(X_train,Y_train)
ped=mod3.predict(X_test)

In [55]: print(classification_report(Y_test,ped))

precision recall f1-score support

0 0.97 1.00 0.99 67

1 1.00 0.96 0.98 47

accuracy 0.98 114

macro avg 0.99 0.98 0.98 114
weighted avg 0.98 0.98 0.98 114

In [56]: c2=confusion_matrix(Y_test,ped)
sns.heatmap(c2,annot=True)

Out[56]: <AxesSubplot:>

In [57]: print(accuracy_score(Y_test,ped))

0.9824561403508771
APPLYING DECISION TREE CLASSIFIER

In [58]: mod=DecisionTreeClassifier()
mod.fit(X_train,Y_train)
p=mod.predict(X_test)

In [59]: print(classification_report(Y_test,p))

precision recall f1-score support

0 0.94 0.90 0.92 67

1 0.86 0.91 0.89 47

accuracy 0.90 114

macro avg 0.90 0.91 0.90 114
weighted avg 0.91 0.90 0.90 114

In [60]: print(accuracy_score(Y_test,p))

0.9035087719298246

In [61]: c2=confusion_matrix(Y_test,p)
sns.heatmap(c2,annot=True)

Out[61]: <AxesSubplot:>