Bayesian data analysis1

Bayesian Data Analysis
By.Dr.Sarita Tripathy
Assistant Professor
School of Computer Engineering
KIIT Deemed to be University

Bayesian Data Analysis
• BDA deals with a set of practical methods for making inferences from
the available data.
• These methods use probability models to model the given data and
also predict future values.
• Bayesian analysis is a statistical paradigm that answers research
questions about unknown parameters using probability statements. For
example, what is the probability that the average male height is
between 70 and 80 inches or that the average female height is between
60 and 70 inches?
• Identify the data, define a descriptive model, specify a prior, compute
the posterior distribution, interpret the posterior distribution, and,
check that the model is a reasonable description of the data.

Steps in BDA
1.BDA consists of three steps:
1.Setting up the prior distribution:
• The domain expertise and prior knowledge is used to develop join probability
distribution
• for all parameters of data under consideration and also output data(which needs to
be predicted) this is termed as prior distribution.
2.Setting up the posterior distribution:
• After taking into account the observed data(given dataset)calculating and
interpreting the appropriate posterior distribution is done.This is estimating the
conditional probability distribution of the data.
3.Evaluating the fit of the model

INTRODUCTION
• Bayesian inference is a method of statistical inference in which
Bayes' theorem is used to update the probability for a hypothesis as
more evidence or information becomes available.
• Bayesian inference is an important technique in statistics, and
especially in mathematical statistics.
• Bayesian inference has found application in a wide range of
activities, including science, engineering, philosophy, medicine,
sport, and law.
• In the philosophy of decision theory, Bayesian inference isclosely
related to subjective probability, often called "Bayesianprobability".

• Bayes theorem adjusts probabilities given new evidence in the
following way:
P(H0|E)= P(E|H0) P(H0)/ P(E)
• Where, H0 represents the hypothesis, called a null hypothesis,
inferred before new evidence
• P(H0) is called the prior probability of H0.
• P(E|H0) is called the conditional probability
• P(E) is called the marginal probability of E: the probability of
witnessing the new evidence.
• P(H0|E) is called the posterior probability of H0 given E.
• The factor P(E|H0) P(E) represents the impact that the
evidence has on the belief in the hypothesis.

• Multiplying the prior probability P(H0) by the factor
P(E|H0)/P(E) will never the yield a probability that is greater
than 1.
• Since P(E) is at least as great as P(E∩H0), which equals to
P(E|H0). P(H0), replacing P(E) with P(E∩H0) in the factor
P(E|H0)/P(E) will yield a posterior probability of 1.
• Therefore, the posterior probability could yield a probability
greater than 1 only if P(E) were less than P(E∩H0) which is
never true.

LIKELIHOOD FUNCTION
• The probability of E given H0, P(E|H0), can be represented as
function of its second argument with its first argument held at
a given value. Such a function is called likelihood function; it
is a function of H0 given E. A ratio of two likelihood functions
is called a likelihood ratio,
˄=L(H0|E)/L(not H0|E)=P(E|H0)/P(E| not H0)
• The marginal probability, P(E), can also be represented as the
sum of the product of all probabilities of mutually exclusive
hypothesis and corresponding conditional probabilities:
P(E| H0) P(H0)+ P(E| not H0) P(not H0)

• As a result, we can rewrite Bayes Theorem as
P(H0|E)=P(E|H0) P(H0)/P(E|H0) P(H0)+ P(E| not H0) P(not
H0)- ˄P(H0)/˄P(H0)| P(not H0)
• With two independent pieces of evidence E1 and E2, Bayesian
inference can be applied iteratively.
• We could use the first piece of evidence to calculate an initial
posterior probability, and then use that posterior probability as
a new prior probability to calculate a second posterior
probability given the second piece of evidence.

From which bowl is the cookie?
• Suppose there are two full bowls of cookies. Bowl #1 has 10
chocolate chip and 30 plain cookies, while bowl #2 has 20 of each.
Our friend Hardika picks a bowl at random, and then picks a cookie
at random. We may assume there is no reason to believe Hardika
treats one bowl differently from another, likewise for the cookies.
The cookie turns out to be a plain one. How probable is it that
Hardika picked it out of bowl #1?
Bowl#1 Bowl#2

• Intuitively, it seems clear that the answer should be more than
a half, since there are more plain cookies in bowl #1.
• The precise answer is given by Bayes' theorem. Let H1
correspond to bowl #1, and H2 to bowl #2.
• It is given that the bowls are identical from Hardika’s point of
view, thus P(H1) = P(H2) and the two must add up to 1, so
both are equal to 0.5.
• The D is the observation of a plain cookie.
• From the contents of the bowls, we know that
P(D| H1)= 30/40= 0.75 and P(D| H2)= 20/40= 0.5

• Bayes formula then yields,
P(H1| D)= P(H1)*P(D|H1)/ P(H1)*P(D|H1)+ P(H2)*P(D|H2)
= 0.5* 0.75/ 0.5*0.75+0.5*0.5
= 0.6
• Before observing the cookie, the probability that Hardika
chose bowl#1 is the prior probability, P(H1) which is 0.5.
After observing the cookie, we revise the probability as 0.6.
• Its worth noting that our belief that observing the plain cookie
should somewhat affect the prior probability P(H1) has formed
the posterior probability P(H1| D), increased from 0.5 to 0.6

• This reflects our intuition that the cookie is more likely from
the bowl#1, since it has a higher ratio of plain to chocolate
cookies than the other.

PRIOR PROBABILITY DISTRIBUTION
• In Bayesian statistical inference, a prior probability
distribution, often called simply the prior, of an uncertain
quantity p( For e.g. suppose p is the proportion of voters who
will vote for Mr. Narendra Modi in a future election) is the
probability distribution that would express ones uncertainty
about p before the data (For e.g. an election poll) are taken into
account.
• It is meant to attribute uncertainty rather than randomness to
the uncertain quantity.

INTRODUCTION TO NAIVE BAYES
• Suppose your data consist of fruits, described by their color
and shape.
• Bayesian classifiers operate by saying “If you see a fruit that is
red and round, which type of fruit most likely to be, based on
the observed data sample? In future, classify red and round
fruit as that type of fruit.”
• A difficulty arises when you have more than a few variables
and classes- you would require an enormous number of
observations to estimate these probabilities.

• Naïve Bayes classifier assume that the effect of a variable
value on a given class is independent of the values of other
variable.
• This assumption is called class conditional independence.
• It is made to simplify the computation and in this sense
considered to be Naïve.

APPLICATIONS
1. Computer applications
• Bayesian inference has applications in artificial
intelligence and expert systems.
• Bayesian inference techniques have been a fundamental
part of computerized pattern recognition techniques since
the late 1950s.
• Recently Bayesian inference has gained popularity among
the phylogenetics community for these reasons; a number
of applications allow many demographic and evolutionary
parameters to be estimated simultaneously.

2. Bioinformatics applications
• Bayesian inference has been applied in different
Bioinformatics applications, including differentially
gene expression analysis, single-cell classification,
cancer subtyping, and etc.

ADVANTAGES
• Including
prediction.
• Including
good information should improve
structure can allow the method to
incorporate more data (for example, hierarchical
modeling allows partial pooling so that external data
can be included in a model even if these external
data share only some characteristics with the current
data being modeled).

DISADVANTAGES
• If the prior information is wrong, it can send
inferences in the wrong direction.
• Bayes inference combines different sources of
information; thus it is no longer an
encapsulation of a particular dataset (which is
sometimes desired, for reasons that go beyond
immediate predictive accuracy and instead
touch on issues of statistical communication).

Naïve Bayesian Classifier
CS 40003: Data Analytics 23
Naïve Bayesian classifier calculate this posterior probability using Bayes’ theorem, which
is as follows.
From Bayes’ theorem on conditional probability, we have
𝑃 𝑌 𝑋 =
𝑃(𝑋|𝑌)∙𝑃(𝑌)
𝑃(𝑋)
=
𝑃(𝑋|𝑌) ∙ 𝑃(𝑌)
𝑃 𝑋 𝑌 = 𝑦1 ∙ 𝑃 𝑌 = 𝑦1 + ⋯ + 𝑃 𝑋 𝑌 = 𝑦𝑘 ∙ 𝑃 𝑌 = 𝑦𝑘
where,
𝑃 𝑋 = σ𝑖=1
𝑘
𝑃(𝑋|𝑌 = 𝑦𝑖) ∙ 𝑃(Y = 𝑦𝑖)
Note:
 𝑃 𝑋 is called the evidence (also the total probability) and it is a constant.
 The probability P(Y|X) (also called class conditional probability) is therefore
proportional to P(X|Y)∙ 𝑃(𝑌).
 Thus, P(Y|X) can be taken as a measure of Y given that X.
P(Y|X) ≈ 𝑃 𝑋 𝑌 ∙ 𝑃(𝑌)

Suppose, for a given instance of X (say x = (𝑋1 = 𝑥1) and ….. (𝑋𝑛= 𝑥𝑛)).
There are any two class conditional probabilities namely P(Y= 𝑦𝑖|X=x) and P(Y=
𝑦𝑗 | X=x).
If P(Y= 𝑦𝑖 | X=x) > P(Y= 𝑦𝑗 | X=x), then we say that 𝑦𝑖 is more stronger than 𝑦𝑗 for
the instance X = x.
The strongest 𝑦𝑖 is the classification for the instance X = x.

Naive Bayesian Classifier
25
Example: With reference to the Air Traffic Dataset mentioned earlier, let us tabulate all the posterior
and prior probabilities as shown below.
Class
Attribute On Time Late Very Late Cancelled
Day
Weekday 9/14 = 0.64 ½ = 0.5 3/3 = 1 0/1 = 0
Saturday 2/14 = 0.14 ½ = 0.5 0/3 = 0 1/1 = 1
Sunday 1/14 = 0.07 0/2 = 0 0/3 = 0 0/1 = 0
Holiday 2/14 = 0.14 0/2 = 0 0/3 = 0 0/1 = 0
Season
Spring 4/14 = 0.29 0/2 = 0 0/3 = 0 0/1 = 0
Summer 6/14 = 0.43 0/2 = 0 0/3 = 0 0/1 = 0
Autumn 2/14 = 0.14 0/2 = 0 1/3= 0.33 0/1 = 0
Winter 2/14 = 0.14 2/2 = 1 2/3 = 0.67 0/1 = 0

Instance:
Case1: Class = On Time : 0.70 × 0.64 × 0.14 × 0.29 × 0.07 = 0.0013
Case2: Class = Late : 0.10 × 0.50 × 1.0 × 0.50 × 0.50 = 0.0125
Case3: Class = Very Late : 0.15 × 1.0 × 0.67 × 0.33 × 0.67 = 0.0222
Case4: Class = Cancelled : 0.05 × 0.0 × 0.0 × 1.0 × 1.0 = 0.0000
Case3 is the strongest; Hence correct classification is Very Late
Week Day Winter High Heavy ???

Note: σ 𝒑𝒊 ≠ 𝟏, because they are not probabilities rather
proportion values (to posterior probabilities)
Input: Given a set of k mutually exclusive and exhaustive classes C =
𝑐1, 𝑐2, … . . , 𝑐𝑘 , which have prior probabilities P(C1), P(C2),….. P(Ck).
There are n-attribute set A = 𝐴1, 𝐴2, … . . , 𝐴𝑛 , which for a given instance have
values 𝐴1 = 𝑎1, 𝐴2 = 𝑎2,….., 𝐴𝑛 = 𝑎𝑛
Step: For each 𝑐𝑖 ∈ C, calculate the class condition probabilities, i = 1,2,…..,k
𝑝𝑖 = 𝑃 𝐶𝑖 × ς𝑗=1
𝑛
𝑃(𝐴𝑗 = 𝑎𝑗|𝐶𝑖)
𝑝𝑥 = max 𝑝1, 𝑝2, … . . , 𝑝𝑘
Output: 𝐶𝑥 is the classification
Algorithm: Naïve Bayesian Classification

Pros and Cons
The Naïve Bayes’ approach is a very popular one, which often works well.
However, it has a number of potential problems
It relies on all attributes being categorical.
If the data is less, then it estimates poorly.

Approach to overcome the limitations in Naïve Bayesian Classification
Estimating the posterior probabilities for continuous attributes
In real life situation, all attributes are not necessarily be categorical, In fact, there is a mix of both
categorical and continuous attributes.
In the following, we discuss the schemes to deal with continuous attributes in Bayesian classifier.
1. We can discretize each continuous attributes and then replace the continuous
values with its corresponding discrete intervals.
2. We can assume a certain form of probability distribution for the continuous variable and
estimate the parameters of the distribution using the training data. A Gaussian
distribution is usually chosen to represent the posterior probabilities for continuous
attributes. A general form of Gaussian distribution will look like
P x: μ, σ2
=
1
2πσ
e−
x − μ 2
2σ2
where, μ and σ2
denote mean and variance, respectively.

For each class Ci, the posterior probabilities for attribute Aj (it is the numeric
attribute) can be calculated following Gaussian normal distribution as follows.
P Aj = aj|Ci =
1
2πσij
e−
aj − μij 2
2σij
2
Here, the parameter μij can be calculated based on the sample mean of attribute
value of Aj for the training records that belong to the class Ci.
Similarly, σij
2 can be estimated from the calculation of variance of such training
records.

Bayesian data analysis1

More Related Content

What's hot (20)

Similar to Bayesian data analysis1 (20)

Recently uploaded (20)

Bayesian data analysis1