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Application of Bayesian Analysis in Medical Diagnosis

Article  in  Journal of the Practice of Cardiovascular Sciences · December 2019

DOI: 10.4103/jpcs.jpcs_51_19

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Application of Bayesian Analysis in Medical Diagnosis

Vivek Verma, Ashwani Kumar Mishra1, Rajiv Narang2
Departments of Neurology and Cardiology, All India Institute of Medical Sciences, 1National Drug Dependence Treatment Centre, All India Institute of Medical
2

Sciences, New Delhi, India

Abstract
In this work, we outlined the application of the Bayesian technique for integrating the results of multiple tests while treating any disease. We
provided an overview of the fundamental concept of Bayesian analysis in making an inference about a phenomenon using a concordance
between available information and prior knowledge. An attempt is being made to demonstrate the applicability using core aspects, viz.,
nature of probability, parameters, and inferential procedure used to draw inference about the population characteristic under both paradigms.
Here, we tried to sketch the underlying steps and assumptions regarding use of the Bayes theorem and the analytical techniques that can
be used to analyze and interpret medical data while treating any disease.

Keywords: Bayes factor, Chi‑square tests, confidence interval, credible interval, posterior distribution, P value

Introduction of myocardial infarction, a medical researcher conducted a

In medical treatments, clinicians and nurses very often have to
make various complex and critical decisions during the diagnosis
of the patients. In reality, these decisions are full of uncertainty
and unpredictability. However, based on the available
information, obtained from various clinical and diagnostic
tests and situation of the patient, both clinicians and nurses try
to reduce their uncertainty in clinical decisions and attempts
to shift to the predictability of the chance of improvement in
patient’s condition. Here, best estimates are obtained using the
available information on clinical and diagnostic tests, and the
situation of the patient acted as light of evidence while making a
decision. For the clinicians, it is of more concerned that they are
capable enough in understanding and interpreting the importance
of prediction probability of particular outcomes based on the
recommended clinical and diagnostic tests. The scenario can be
visualized through Example 1, where a researcher is interested
in determining the association of smoking as a risk factor for
the development of myocardial infarction [Table 1].
Example 1
Myocardial infarction is one of the most leading causes of
death worldwide from coronary artery disease (CAD). Existing
literature has shown that risk for myocardial infarction is
higher among smokers compared to nonsmokers. To determine
the association of smoking as risk factor for development
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case–control study on 100 patients, where 50 patients with
myocardial infarction within 1 year on onset and 50 controls
were recruited from a tertiary care hospital [Table 1]. Suppose
p1 is the proportion of patients in control group affected from
myocardial infarction and p2 as the same for group exposed.
He hypothesized his perception under null as the occurrence of
myocardial infarction is independent of smoking habit against
one‑sided alternative as myocardial infarction is higher among
smokers than nonsmokers.
H 0 : p1  p 2 vs.H1 : p1  p 2
In the control group, 0 myocardial infarction cases are found;
in the exposed group, there are three. As P = 0.1212, based on
one‑sided Fisher’s exact test, is greater than 0.05 significance
level, we do not reject the null hypothesis that the smoking
habit is independent of myocardial infarction.
Address for correspondence: Dr. Rajiv Narang,
Department of Cardiology, All India Institute of Medical Sciences,
Ansari Nagar, New Delhi ‑ 110 029, India.
E‑mail: r_narang@yahoo.com
Date of Submission: 16‑Aug‑2019 Date of Acceptance: 26-Nov-2019
Date of Revision: 26-Sep-2019 Date of Web Publication: 20-Dec-2019
This is an open access journal, and articles are distributed under the terms of the Creative
Commons Attribution‑NonCommercial‑ShareAlike 4.0 License, which allows others to
remix, tweak, and build upon the work non‑commercially, as long as appropriate credit
is given and the new creations are licensed under the identical terms.
For reprints contact: reprints@medknow.com

DOI: How to cite this article: Verma V, Mishra AK, Narang R. Application
10.4103/jpcs.jpcs_51_19 of Bayesian analysis in medical diagnosis. J Pract Cardiovasc Sci
2019;5:136-41.

136 © 2019 Journal of the Practice of Cardiovascular Sciences | Published by Wolters Kluwer - Medknow
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Verma, et al.: Bayesian analysis in medical diagnosis
Clinical decisions are based on the probability theory because
it acts as a key element required to establish a process of
reasoning.[1] The challenges that occurred to clinicians and
nurses are in estimating the probability based on the process
and its related quantification by relating the proposition
obtained from the available information with the values of
probabilities.[2]
In medical diagnosis, the probability defined as the “degree
of belief” or plausibility that supports the given proposition
as the decision. The decisions are made using the prior
experiences and support of available information in terms of
various diagnostic and medical records. The situation can be
understood practically, using Example 2 as an extension of
Example 1.
Example 2 (continuation of Example 1)
A cardiologist may claim that three myocardial infarction cases
in 50  patients are definitely in cardiological aspects being
significant. This belief may be based on the information from
another study in the same department in the previous year in
which myocardial infarction has never shown up in control
patients. If there were 400 historical controls in addition to
the 50 concurrent controls, none with myocardial infarction,
then the contingency table takes the following form Table 2.
Now, the one‑sided P value = 0.0009, based on one‑sided
Fisher’s exact test, is less than 0.05 significance level, we reject
the null hypothesis that the smoking habit is independent of
the myocardial infarction, which makes both the statistical and
cardiological importance more compatible.
In one context, Example 2 as compared to Example 1, we
have shown that the decision based on frequentist principle
may change from acceptance to rejection, whereas the other
aspect which suggests incorporation of existing information
along with the obtained information will help to achieve a more
realistic conclusion. In the frequentist paradigm, it is generally
inappropriate[3,4] to gather historical and concurrent information
and to quantify one’s prior experiences and learning’s in light
of available information.
In frequentist statistics, the probability of occurrence of an
event is defined in the long run of the experiment (i.e., the
experiment is repeated under the same conditions to obtain
the outcome).
Example 3
Let us consider that a coin is tossed and our interest lies in
estimation of the fairness of the coin, as presented in Table 3.
To check the unbiased behavior of the coin, the experiment is
theoretically repeated infinite number of times but practically
done with a stopping intention.
As we know that probability of getting a head on tossing a
fair coin is 0.5, then the number of heads will represent the
actual number of heads obtained. Here, difference denotes the
difference between 0.5 times (number of tosses) − number of
heads obtained [Table 3].
Journal of the Practice of Cardiovascular Sciences  ¦  Volume 5 ¦ Issue 3 ¦ September-December 2019
An important thing is to note that, though the difference
between the actual number of heads and expected number of
heads (50% of number of tosses) increases as the number of
tosses are increased, the proportion of number of heads to total
number of tosses approaches to 0.5 (for a fair coin). However,
based on the frequentist principle, it is not possible to estimate
or update the unbiasedness of the coin using the limited tosses,
and theoretically repeating the experiment infinite number of
times is practically impossible.
To incorporate the prior experience with the available
information, statisticians tried for alternative procedures that
will update their knowledge based on the available evidence
so that decisions became more effective and certain. The
Bayesian method was an outcome of such an effort. This
procedure was introduced by Thomas Bayes and Laplace in
the 18th century and developed by statisticians and philosophers
in the 20th century. Bayesian approaches were considered as
the mathematical manipulation of uncertainty as it provides
a way of reasoning coherently in the world around us, in the
face of uncertainty,[5] where probabilities are quantified by
the plausibility or truth of a suggestion that is conditional on
the available or gathered information.[1]
The probability interpretation of an event can be understood in two
ways: first, through direct ways (frequentist), where we know the
previous circumstances and required the probability of an event,
and second, through unconventional ways by using the inverse
method (Bayesian), where we know the event which has happened
and requires the probability which is resulted from any particular
set of circumstances under which it might have happened.
Example 4
The probability of a certain medical test being positive is 90% if
a patient has disease. 1% of the population has the disease, and
the test records a false positive 5% of the time. If we receive a
positive test, what is our probability of having disease?
According to the frequentist way of defining, the probability
of having disease is 1%, as either the person has the disease
or not. On the other hand, the Bayesian suggests that there is
a prior probability of 1% that the person has the disease. This
probability should be updated in light of the new data as
P(Test  | Disease)  0.9, P( Disease)  0.01,
P(Test  | no Disease)  0.05,
we can obtain the probability that the person, whose test was
positive and also has the disease, i.e., P(Disease | Test+) as
P  Disease  P  Test+|Disease 
P  Disease|Test+  
P  Test+ 
P  Disease  P  Test+|Disease 

P  Disease  P  Test+|Disease  
P  No Disease  P  Test+|No Disease 
 0.15.
137
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Verma, et al.: Bayesian analysis in medical diagnosis
The result suggests that probability that the person has the
disease given that the test was found to be positive is 15%.
Bayes theorem has used widely to draw inferences in various
clinical trials[3,6] and healthcare evaluation.[7] Among various
applications of Bayes’ theorem has also used for outcomes’
analysis and assessments such as cardiac arrest,[8] stress
testing,[9] estimation of cardiac biventricular volumes,[10]
perioperative cardiac risk assessment,[11] percutaneous coronary
intervention strategies in cardiogenic shock,[12] and evaluation
of the noninferiority of transcatheter aortic valve replacement as
compared with surgical valve replacement[13] and its application
in stress electrocardiography, thallium scintigraphy, technetium
blood‑pool scintigraphy, and cardiac fluoroscopy.[14]
The present work outlined an overview of methodological
aspects of the Bayesian technique and compared the classical
or frequentist approach. Section 2 presented a summary of
introductory background about the definition of probability
based on the Bayes theorem. The differences in the Bayesian
and frequentist approaches are presented in Section 3. This
section discussed how Bayesian and frequentist methods
define probability, estimation procedures, and performance
evaluation.
Fundamentals of Bayesian Methodology
There is no fundamental distinction between unobserved events
and unknown parameter of interest in the Bayesian paradigm
and are defined using the available quantities and information
required to describe probability of occurrence of that event.
In, the existing information available before observing data
is called prior distribution, and after observing the data, the
update in the information due to additional information of data
is called posterior distribution. The distributional assumptions
that lead to obtaining inferences in Bayesian procedure are as
follows:[15,16]
1. A specific parametric form is essential to describe the
distribution of the observations given the parameter value,
which is commonly known as a likelihood function
2. Since the parameter is assumed as an unknown quantity
rather than being fixed as of classical inference, the prior
distribution on the parameter of interest unconditional on
the data must be given.
The essential steps that usually followed to draw inferences
about the characteristic of the unknown parameter under the
Bayesian thinking are:
1. Specify a probability model, which contains some prior
information about the unknown parameter
2. Update information about the unknown parameter through
conditioning their probability model given the observed
data. Here, the data values are assumed to be exchangeable,
i.e., the model will not be changed by reordering the data
value. This exchangeability assumption assures that the
data generation process is conditional on the unknown
model parameter and will be the same for every generated
data
138 Journal of the Practice of Cardiovascular Sciences  ¦  Volume 5  ¦  Issue 3  ¦  September-December 2019
3. Evaluate the performance of the model to the available
or observed data and sensitivity of the conclusion to the
assumption about the model.
Methodologically, Bayesian modeling and Bayesian data
analysis are approaches of incorporation of prior information
and utilization of observed data to draw inference about the
parameters. Here, data are stored as a likelihood function,
which describes the strength of support obtained from the
observations for the various possible values of the parameter.
In the Bayesian paradigm, the prior information about the
unknown parameter of the statistical model plays a very
crucial role, which needs to be identified and expressed in the
form of a prior distribution. Generally, prior distributions are
classified as either informative prior, where prior information
is genuine and provides the best explanations of its strength
and relation to the observed data, or noninformative prior
that are also known as improper or weak prior, where the
credibility of prior information is lacking and is defined
based on the belief before obtaining the new data. This
information obtained from the prior and the data are
then synthesized to produce posterior distribution, which
expresses the enhancement in the knowledge about the
parameter after obtaining the data. Bayesian methodology
can be mathematically formulated as, if D denotes the data
point and θ some model parameter,
P  D |   P ( )
P  | D   (1)
 P  D |   P   d
.

Where P(θ) is the prior probability of θ before observing any
information about D, P (D|θ) is the likelihood function which
denotes the probability of observing D conditioned on θ, and
P(θ|D) is the posterior probability of θ after observing D.
Methodological Differences in Paradoxes of
Frequentist and Bayesian Paradigm
One of the main objectives of medical research is to infer a
population phenomenon based on the information available in
terms of some data from it. For exploring more information
about the behavior and pattern of changes in the population
characteristic(s) using the available or obtained sample,
in addition to classical summaries, a specific branch of
statistics deals with that is called the inferential statistics.
In inferential statistical, we expand our horizon beyond the
classical statistics with various techniques of estimation of
parameters, comparison of their closeness, and changes with
population value. There are two different philosophical aspects
of inferential statistics, viz., classical or frequentist inference
and Bayesian inference.
For clarity under the Bayesian approach, we first need to
understand the basic differences between Bayesian and
frequentist inference. This section addressed the nature
of probability, parameters, and inferences under the two
approaches. In the Bayesian paradigm parameter of interest,
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Verma, et al.: Bayesian analysis in medical diagnosis

θ, is assumed as an unknown quantity rather than being fixed
as of frequentist methodology. The core difference between
Bayesian and frequentist methodologies in contrast to the
estimation of the parameter of interest says θ. In the present
section, we highlighted some of the important aspects, viz.,
nature of probability, parameters, and inferential procedure
used to draw inference about the population characteristic
under both Bayesian and frequentist based on the obtained
samples. The core differences are as follows:
Interpretation of probability
Frequentist defined probability as the number of times an event
observed (D) when an infinite series of the trial has performed
under identical situation and condition and usually symbolized
as P(D|θ). However, in Bayesian paradigm,[2] probability is
defined as degree of belief of the observer before or after the
data observed.
The definition of probability as stated in Bayes theorem of
equation (1) is subjective and not the same as objectively
(frequentist) defined as “the relative frequency of an occurrence
of the event from a large number of repeated trials.” The
frequentist definition raised some interesting epistemological
issues regarding probability theory, such as how one can define
the probability density function of a parameter on the basis
a single data set. These questions can easily address using
Bayesian interpretation of probability.
The basic difference between frequentist and Bayesian
methodology was that frequentist defines probability as
the frequency of repeated occurrence of an event (perhaps
hypothetical), whereas for Bayesians, probability is defined as
the degree of certainty of the occurrence of an event. Broadly
speaking, for frequentist model, parameters are fixed quantities
and data are random; on the other hand, for Bayesians model,
parameter(s) is a random quantity and data are considered as fixed.
Example 5
To detect the CAD (D), usually cardiac fluoroscopy (T)
test is opted, where the number of major coronary arteries
(left anterior descending, circumflex, and right coronary
artery) was reviewed in the routine heart’s fluoroscopy
to trace the deposition of radiodense[14] in the heart. The
available information, which was obtained in terms of
sensitivity, (P[T+|D+]), specificity,  (P[T−|D−]), and prior
information (pretest likelihood) such as chance of occurrence
of CAD, P(D+), under Bayesian paradigm, was utilized to
calculate the posttest likelihood for the occurrence of CAD as.
P  D | T   
P  D   [ P(T  | D )]
P  D    P T  | D     (1  P  D  )[ P(T  | D )]
The posttest likelihood or posterior probabilities provide
more information than that obtained in pretest likelihood and
available information.
Fixed and variable quantities
In frequentist methodology, the obtained observations have
considered as an independent and identically distributed
random sample from a population, where the population
parameters are unknown but fixed by nature. On the other
hand, in Bayesian analysis, the observed data are considered
as fixed quantity or realization of the population characteristic.
Here also, the parameters are unknown but random quantities
and described distributionally.
Summary of the estimators
In frequentist approach, point estimates and their standard errors,
along with the 95% confidence interval, describe not only the
characteristics of the estimator but also the interval that covers
the true parameter value 95% of times, on an average. In the
Bayesian analysis, the inference about the parameter is usually
obtained through their posterior means and quantiles. The highest
probability density interval indicates the region of highest posterior
probability of occurrence of the parameter. The Bayesian credible
interval provides a probabilistic bounded region for the parameter
value. However, the frequentist confidence interval describes a
probability about the bounds given fixed parameter value.
Example 6
To estimate the incidence of CAD in people without any
heart disease at baseline but having snorers with obstructive
sleep apnea and snorers without obstructive sleep apnea,
a study was conducted[17] on a total of 308 (245 males and

a b
Figure 1: Density pattern of binomial likelihood, beta prior, and beta‑binomial posterior distribution. (a) Snores with obstructive sleep apnea, (b) snores
without obstructive sleep apnea.

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Verma, et al.: Bayesian analysis in medical diagnosis

63 females) individuals reported in middle‑aged males P( EF )

during a follow‑up period of 7 years. Let us consider that the PF | E  0.67
P( E )
occurrence of any CAD among those having (a) snorers with
obstructive sleep apnea and (b) snorers without obstructive However, the conditional probability that an individual
sleep apnea, is a Binomial random variable, and the incidence progesterone receptor, given the tumor is estrogen
rate has assumed to follow beta (a, b), for the present study: receptor‑negative, is
a = 4 and b = 22. The impact on change in the posterior
distribution (beta‑binomial) for the proportion of people
Table 1: Cross‑tabulation of smoking habit with
who suffered from CAD due to different prior choices for the
occurrence of myocardial infarction
given data is presented in Table 4 and presented in Figure 1.
Smoking Myocardial infarction Total
Quality checking
Yes No
In the frequentist paradigm, the comparison between groups
Control 0 50 50
was generally carried out by defining the errors of Type I (level
Exposed 3 47 50
of known significance) and Type II, the size of the effect, and/or
Total 3 97 100
the power of the test procedure. The final inference is based on
the P value.[18] In the case of Bayesian method,[19] the analytical
procedure allows the formal incorporation of prior information. Table 2: Cross‑tabulation of smoking habit with
Here, the comparison between the groups is generally done occurrence of myocardial infarction with additional
by comparing the posterior predictive distributions,[20,21] the controls
posterior sensitivity is based on the prior forms, and the final
Smoking Myocardial infarction Total
inferences were made using the Bayes’ factors.[6,22,23] The
Bayes’ factor (BF01) is the ratio of the posterior odds over Yes No
the ratio of the prior odds. The rule of thumb[23] to infer is as Control 0 450 450
follows, if log10(BF01) varies between 0 and 0.5, the evidence Exposed 3 47 50
against null hypothesis H0 will be poor, if log10(BF01) lies Total 3 497 500
between 0.5 and 1, it is substantial, if it is between 1 and 2, it
is strong, and if it is above 2, it is decisive. Table 3: The frequency distribution of heads tossed from
To demonstrate the practical significance and applicability a fair coin
of the Bayesian method, we discussed through below given Number of tosses Number of heads Difference from fairness
example of estrogen and progesterone receptors status of tumor 10 3 2
assessed from 20 breast cancer patients. 50 24 1
Example 7 100 47 3
500 258 −8
Suppose the estrogen and progesterone receptors status of the
1000 514 −14
tumor are assessed from 20 patients with locally advanced
5000 2448 52
breast cancer patients. Here, we are trying to test whether
10,000 4947 53
the estrogen and progesterone receptors status of tumor are
independent [Table 5].
As the P = 0.05402, based on the Chi‑square test, is greater than Table 4: Summary statistics of prior, likelihood, and
0.05 significance level, we do not reject the null hypothesis that posterior distributions
the status of progesterone and estrogen receptors is independent Mean±SD
among breast cancer patients. Prior Likelihood Posterior
Let E be the event that the tumor is estrogen receptor‑positive Snorers with 0.154±0.070 0.168±0.036 0.160±0.032
and F be the event that it is progesterone receptor‑positive. obstructive sleep apnea
Snorers without 0.154±0.070 0.059±0.0164 0.066±0.0160
Then,
obstructive sleep apnea
SD: Standard deviation
8 4
P  E   P  EF   P  EF '    0.60
20 20
Table 5: Cross‑tabulation of status of estrogen and
8 1
P  F   P  EF   P  E ' F     0.45 progesterone receptors among breast cancer patients
20 20
Estrogen Progesterone
8
P  EF   Positive Negative
20
The conditional probability that an individual progesterone Positive 8/20 4/20
receptor, given the tumor is estrogen receptor‑positive, is Negative 1/20 7/20

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Verma, et al.: Bayesian analysis in medical diagnosis

P  F | E ' 
P( E ' F )
 0.125
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