7. Write a program to construct a Bayesian network considering medical data.
Use this model
to demonstrate the diagnosis of heart patients using standard Heart Disease Data Set. You can
use Java/Python ML library classes/API
Theory
A Bayesian network is a directed acyclic graph in which each edge corresponds to a conditional
dependency, and each node corresponds to a unique random variable.
Bayesian network consists of two major parts: a directed acyclic graph and a set of conditional
probability distributions
The directed acyclic graph is a set of random variables represented by nodes.
The conditional probability distribution of a node (random variable) is defined for every
possible outcome of the preceding causal node(s).
For illustration, consider the following example. Suppose we attempt to turn on our computer,
but the computer does not start (observation/evidence). We would like to know which of the
possible causes of computer failure is more likely. In this simplified illustration, we assume
only two possible causes of this misfortune: electricity failure and computer malfunction.
The corresponding directed acyclic graph is depicted in below figure.
Fig: Directed acyclic graph representing two independent possible causes of a computer failure.
The goal is to calculate the posterior conditional probability distribution of each of the possible
unobserved causes given the observed evidence, i.e. P [Cause | Evidence].
Data Set:
Title: Heart Disease Databases
The Cleveland database contains 76 attributes, but all published experiments refer to using a
subset of 14 of them. In particular, the Cleveland database is the only one that has been used
by ML researchers to this date. The "Heartdisease" field refers to the presence of heart disease
in the patient. It is integer valued from 0 (no presence) to 4.
Database: 0 1 2 3 4 Total
Cleveland: 164 55 36 35 13 303
Attribute Information:
1. age: age in years
2. sex: sex (1 = male; 0 = female)
3. cp: chest pain type
Value 1: typical angina
Value 2: atypical angina
Value 3: non-anginal pain
Value 4: asymptomatic
4. trestbps: resting blood pressure (in mm Hg on admission to the hospital)
5. chol: serum cholestoral in mg/dl
6. fbs: (fasting blood sugar > 120 mg/dl) (1 = true; 0 = false)
7. restecg: resting electrocardiographic results
Value 0: normal
Value 1: having ST-T wave abnormality (T wave inversions and/or ST elevation
or depression of > 0.05 mV)
Value 2: showing probable or definite left ventricular hypertrophy by Estes'
criteria
8. thalach: maximum heart rate achieved
9. exang: exercise induced angina (1 = yes; 0 = no)
10. oldpeak = ST depression induced by exercise relative to rest
11. slope: the slope of the peak exercise ST segment
Value 1: upsloping
Value 2: flat
Value 3: downsloping
12. ca = number of major vessels (0-3) colored by flourosopy
13. thal: 3 = normal; 6 = fixed defect; 7 = reversable defect
14. Heartdisease: It is integer valued from 0 (no presence) to 4. Diagnosis of heart disease
(angiographic disease status)
Some instance from the dataset:
age sex cp trestbps chol fbs restecg thalach exang oldpeak slope ca thal Heartdisease
63 1 1 145 233 1 2 150 0 2.3 3 0 6 0
67 1 4 160 286 0 2 108 1 1.5 2 3 3 2
67 1 4 120 229 0 2 129 1 2.6 2 2 7 1
41 0 2 130 204 0 2 172 0 1.4 1 0 3 0
62 0 4 140 268 0 2 160 0 3.6 3 2 3 3
60 1 4 130 206 0 2 132 1 2.4 2 2 7 4
Program:
import numpy as np
import csv
import pandas as pd
from pgmpy.models import BayesianModel
from pgmpy.estimators import MaximumLikelihoodEstimator
from pgmpy.inference import VariableElimination
#read Cleveland Heart Disease data
heartDisease = pd.read_csv('heart.csv')
heartDisease = heartDisease.replace('?',np.nan)
#display the data
print('Few examples from the dataset are given below')
print(heartDisease.head())
#Model Bayesian Network
Model=BayesianModel([('age','trestbps'),('age','fbs'),
('sex','trestbps'),('exang','trestbps'),('trestbps','heartdise
ase'),('fbs','heartdisease'),('heartdisease','restecg'),
('heartdisease','thalach'),('heartdisease','chol')])
#Learning CPDs using Maximum Likelihood Estimators
print('\n Learning CPD using Maximum likelihood estimators')
model.fit(heartDisease,estimator=MaximumLikelihoodEstimator)
# Inferencing with Bayesian Network
print('\n Inferencing with Bayesian Network:')
HeartDisease_infer = VariableElimination(model)
#computing the Probability of HeartDisease given Age
print('\n 1. Probability of HeartDisease given Age=30')
q=HeartDisease_infer.query(variables=['heartdisease'],evidence
={'age':28})
print(q['heartdisease'])
#computing the Probability of HeartDisease given cholesterol
print('\n 2. Probability of HeartDisease given cholesterol=100')
q=HeartDisease_infer.query(variables=['heartdisease'],evidence
={'chol':100})
print(q['heartdisease'])
Output:
Few examples from the dataset are given below
age sex cp trestbps ...slope ca thal heartdisease
0 63 1 1 145 ... 3 0 6 0
1 67 1 4 160 ... 2 3 3 2
2 67 1 4 120 ... 2 2 7 1
3 37 1 3 130 ... 3 0 3 0
4 41 0 2 130 ... 1 0 3 0
[5 rows x 14 columns]
Learning CPD using Maximum likelihood estimators
Inferencing with Bayesian Network:
1. Probability of HeartDisease given Age=28
╒════════════════╤═════════════════════╕
│ heartdisease │ phi(heartdisease) │
╞════════════════╪═════════════════════╡
│ heartdisease_0 │ 0.6791 │
├────────────────┼─────────────────────┤
│ heartdisease_1 │ 0.1212 │
├────────────────┼─────────────────────┤
│ heartdisease_2 │ 0.0810 │
├────────────────┼─────────────────────┤
│ heartdisease_3 │ 0.0939 │
├────────────────┼─────────────────────┤
│ heartdisease_4 │ 0.0247 │
╘════════════════╧═════════════════════╛
2. Probability of HeartDisease given cholesterol=100
╒════════════════╤═════════════════════╕
│ heartdisease │ phi(heartdisease) │
╞════════════════╪═════════════════════╡
│ heartdisease_0 │ 0.5400 │
├────────────────┼─────────────────────┤
│ heartdisease_1 │ 0.1533 │
├────────────────┼─────────────────────┤
│ heartdisease_2 │ 0.1303 │
├────────────────┼─────────────────────┤
│ heartdisease_3 │ 0.1259 │
├────────────────┼─────────────────────┤
│ heartdisease_4 │ 0.0506 │
╘════════════════╧═════════════════════╛
