Introduction to Bayesian Inference

5/23/2018 Introduction to Bayesian Inference
https://www.datascience.com/blog/introduction-to-bayesian-inference-learn-data-science-tutorials 1/22
Prerequisites
This post is an introduction to Bayesian probability and inference. We will discuss the intuition
behind these concepts, and provide some examples written in Python to help you get started. To
get the most out of this introduction, the reader should have a basic understanding of statistics
and probability, as well as some experience with Python. The examples use the
Python package pymc3.
Introduction to Bayesian Thinking
USE CASES, LEARN DATA SCIENCE, PYTHON, DATA VISUALIZATION
Introduction to Bayesian
Inference
Aaron Kramer 12.12.16


Bayesian inference is an extremely powerful set of tools for modeling any random variable, such
as the value of a regression parameter, a demographic statistic, a business KPI, or the part of
speech of a word. We provide our understanding of a problem and some data, and in return get
a quantitative measure of how certain we are of a particular fact. This approach to modeling
uncertainty is particularly useful when:
Data is limited
We're worried about overﬁtting
We have reason to believe that some facts are more likely than others, but that
information is not contained in the data we model on
We're interested in precisely knowing how likely certain facts are, as opposed
to just picking the most likely fact
The table below enumerates some applied tasks that exhibit these challenges, and describes
how Bayesian inference can be used to solve them. Don't worry if the Bayesian solutions are
foreign to you, they will make more sense as you read this post:


Typically, Bayesian inference is a term used as a counterpart to frequentist inference. This can be
confusing, as the lines drawn between the two approaches are blurry. The true Bayesian and
frequentist distinction is that of philosophical differences between how people interpret what
probability is. We'll focus on Bayesian concepts that are foreign to traditional frequentist
approaches and are actually used in applied work, speciﬁcally the prior and posterior
distributions.
Consider Bayes' theorem:
Think of A as some proposition about the world, and B as some data or evidence. For example, A
represents the proposition that it rained today, and B represents the evidence that the sidewalk
outside is wet:

p(rain | wet) asks, "What is the probability that it rained given that it is wet outside?" To evaluate
this question, let's walk through the right side of the equation. Before looking at the ground,
what is the probability that it rained, p(rain)? Think of this as the plausibility of an assumption
about the world. We then ask how likely the observation that it is wet outside is under that
assumption, p(wet | rain)? This procedure effectively updates our initial beliefs about a
proposition with some observation, yielding a final measure of the plausibility of rain, given the
evidence.
This procedure is the basis for Bayesian inference, where our initial beliefs are represented by
the prior distribution p(rain), and our final beliefs are represented by the posterior distribution
p(rain | wet). The denominator simply asks, "What is the total plausibility of the evidence?",
whereby we have to consider all assumptions to ensure that the posterior is a proper probability
distribution.
Bayesians are uncertain about what is true (the value of a KPI, a regression coefficient, etc.), and
use data as evidence that certain facts are more likely than others. Prior distributions reflect our
beliefs before seeing any data, and posterior distributions reflect our beliefs after we have
considered all the evidence. To unpack what that means and how to leverage these concepts for
actual analysis, let's consider the example of evaluating new marketing campaigns.
Example: Evaluating New Marketing Campaigns Using Bayesian Inference
Assume that we run an ecommerce platform for clothing and in order to bring people to our site,
we deploy several digital marketing campaigns. These campaigns feature various ad images and
captions, and are presented on a number of social networking websites. We want to present the
ads that are the most successful. For the sake of simplicity, we can assume that the most
successful campaign is the one that results in the highest click-through rate: the ads that are
most likely to be clicked if shown.
We introduce a new campaign called "facebook-yellow-dress," a campaign presented to
Facebook users featuring a yellow dress. The ad has been presented to 10 users so far, and 7 of

the users have clicked on it. We would like to estimate the probability that the next user will click
on the ad.
By encoding a click as a success and a non-click as a failure, we're estimating the probability
θ that a given user will click on the ad. Naturally, we are going to use the campaign's historical
record as evidence. Because we are considering unordered draws of an event that can be either
0 or 1, we can infer the probability θ by considering the campaign's history as a sample from a
binomial distribution, with probability of success θ. Traditional approaches of inference consider
multiple values of θ and pick the value that is most aligned with the data. This is known as
maximum likelihood, because we're evaluating how likely our data is under various assumptions
and choosing the best assumption as true. More formally:
argmax p(X |θ), where X is the data we've observed.
Here, p(X |θ) is our likelihood function; if we ﬁx the parameter θ, what is the probability of
observing the data we've seen? Let's look at the likelihood of various values of θ given the data
we have for facebook-yellow-dress:
θ
import numpy as np
from scipy.misc import factorial
import matplotlib.pyplot as plt
%matplotlib inline
plt.rcParams['figure.figsize'] = (16,7)
def likelihood(theta, n, x):
"""
likelihood function for a binomial distribution
n: [int] the number of experiments
x: [int] the number of successes
theta: [float] the proposed probability of success
"""
return (factorial(n) / (factorial(x) * factorial(n - x)))
* (theta ** x) * ((1 - theta) ** (n - x))
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#the number of impressions for our facebook-yellow-dress campaignn_impressions
#the number of clicks for our facebook-yellow-dress campaign
n_clicks = 7.
#observed click through rate
ctr = n_clicks / n_impressions
#0 to 1, all possible click through rates
possible_theta_values = map(lambda x: x/100., range(100))
#evaluate the likelihood function for possible click through rates
likelihoods = map(lambda theta: likelihood(theta, n, x)
, possible_theta_values)
#pick the best theta
mle = possible_theta_values[np.argmax(likelihoods)]
#plot
f, ax = plt.subplots(1)
ax.plot(possible_theta_values, likelihoods)
ax.axvline(mle, linestyle = "--")
ax.set_xlabel("Theta")
ax.set_ylabel("Likelihood")
ax.grid()
ax.set_title("Likelihood of Theta for New Campaign")
plt.show()
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Of the 10 people we showed the new ad to, 7 of them clicked on it. So naturally, our likelihood
function is telling us that the most likely value of theta is 0.7. However, some of our analysts are
skeptical. The performance of this campaign seems extremely high given how our other
campaigns have done historically. Let's overlay this likelihood function with the distribution of
click-through rates from our previous 100 campaigns:
plt.rcParams['figure.figsize'] = (16, 7)
import numpy as np
import pandas as pd
true_a = 11.5
true_b = 48.5
#number of marketing campaigns
N = 100#randomly generate "true" click through rate for each campaign
p = np.random.beta(true_a,true_b, size=N)
#randomly pick the number of impressions for each campaign
impressions = np.random.randint(1, 10000, size=N)
#sample number of clicks for each campaign
clicks = np.random.binomial(impressions, p).astype(float)
click_through_rates = clicks / impressions
#plot the histogram of previous click through rates with the evidence#of the n
ax.axvline(mle, linestyle = "--")
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Clearly, the maximum likelihood method is giving us a value that is outside what we
would normally see. Perhaps our analysts are right to be skeptical; as the campaign
continues to run, its click-through rate could decrease. Alternatively, this campaign
could be truly outperforming all previous campaigns. We can't be sure. Ideally, we
would rely on other campaigns' history if we had no data from our new campaign. And
zero_to_one = [j/100. for j in xrange(100)]
counts, bins = np.histogram(click_through_rates
, bins=zero_to_one)
counts = counts / 100.
ax.plot(bins[:-1],counts, alpha = .5)
line1, line2, line3 = ax.lines
ax.legend((line2, line3), ('Likelihood of Theta for New Campaign'
, 'Frequency of Theta Historically')
, loc = 'upper left')
ax.grid()
ax.set_title("Evidence vs Historical Click Through Rates")
plt.show()
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as we got more and more data, we would allow the new campaign data to speak for
itself.
The Prior Distribution
This skepticism corresponds to prior probability in Bayesian inference. Before considering any
data at all, we believe that certain values of θ are more likely than others, given what we know
about marketing campaigns. We believe, for instance, that p(θ = 0.2)>p(θ = 0.5), since none of our
previous campaigns have had click-through rates remotely close to 0.5. We express our prior
beliefs of θ with p(θ). Using historical campaigns to assess p(θ) is our choice as a researcher.
Generally, prior distributions can be chosen with many goals in mind:
Informative; empirical: We have some data from related experiments and
choose to leverage that data to inform our prior beliefs. Our prior beliefs will
impact our final assessment.
Informative; non-empirical: We have some inherent reason to prefer certain
values over others. For instance, if we want to regularize a regression to prevent
overfitting, we might set the prior distribution of our coefficients to have
decreasing probability as we move away from 0. Our prior beliefs will impact
our final assessment.
Informative; domain-knowledge: Though we do not have supporting data, we
know as domain experts that certain facts are more true than others. Our prior
beliefs will impact our final assessment.
Non-informative: Our prior beliefs will have little to no effect on our final
assessment. We want the data to speak for itself.
For our example, because we have related data and limited data on the new campaign, we will
use an informative, empirical prior. We will choose a beta distribution for our prior for θ. The
beta distribution is a 2 parameter (α, β) distribution that is often used as a prior for
the θ parameter of the binomial distribution. Because we want to use our previous campaigns as
the basis for our prior beliefs, we will determine α and β by fitting a beta distribution to our
historical click-through rates. Below, we fit the beta distribution and compare the estimated prior
distribution with previous click-through rates to ensure the two are properly aligned:


from scipy.stats import beta
#fit beta to previous CTRs
prior_parameters = beta.fit(click_through_rates
, floc = 0
, fscale = 1)#extract a,b from fit
prior_a, prior_b = prior_parameters[0:2]
#define prior distribution sample from prior
prior_distribution = beta(prior_a, prior_b)
#get histogram of samples
prior_samples = prior_distribution.rvs(10000)
#get histogram of samples
fit_counts, bins = np.histogram(prior_samples
, zero_to_one)#normalize histogram
fit_counts = map(lambda x: float(x)/fit_counts.sum()
, fit_counts)
#plot
ax.plot(bins[:-1], fit_counts)
hist_ctr, bins = np.histogram(click_through_rates
, zero_to_one)
hist_ctr = map(lambda x: float(x)/hist_ctr.sum()
, hist_ctr)
ax.plot(bins[:-1], hist_ctr)
estimated_prior, previous_click_through_rates = ax.lines
ax.legend((estimated_prior, previous_click_through_rates)
,('Estimated Prior'
, 'Previous Click Through Rates'))
ax.grid()
ax.set_title("Comparing Empirical Prior with Previous Click Through Rates")
plt.show()
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We ﬁnd that the best values of α and β are 11.5 and 48.5, respectively. The beta distribution with
these parameters does a good job capturing the click-through rates from our previous
campaigns, so we will use it as our prior. We will now update our prior beliefs with the data from
the facebook-yellow-dress campaign to form our posterior distribution.
The Posterior Distribution
After considering the 10 impressions of data we have for the facebook-yellow-dress campaign,
the posterior distribution of θ gives us plausibility of any click-through rate from 0 to 1.
The effect of our data, or our evidence, is provided by the likelihood function, p(X|θ). What we
are ultimately interested in is the plausibility of all proposed values of θ given our data or our
posterior distribution p(θ|X). From the earlier section introducing Bayes' Theorem, our posterior
distribution is given by the product of our likelihood function and our prior distribution:
Since p(X) is a constant, as it does not depend on θ, we can think of the posterior distribution as:

We'll now demonstrate how to estimate p(θ|X) using PyMC.
Doing Bayesian Inference with PyMC
Usually, the true posterior must be approximated with numerical methods. To see why, let's
return to the deﬁnition of the posterior distribution:
The denominator p(X) is the total probability of observing our data under all possible values of θ.
A more descriptive representation of this quantity is given by:
Which sums the probability of X over all values of θ. This integral usually does not have a closed-
form solution, so we need an approximation. One method of approximating our posterior is by
using Markov Chain Monte Carlo (MCMC), which generates samples in a way that mimics the
unknown distribution. We begin at a particular value, and "propose" another value as a sample
according to a stochastic process. We may reject the sample if the proposed value seems
unlikely and propose another. If we accept the proposal, we move to the new value and propose
another.
PyMC is a python package for building arbitrary probability models and obtaining samples from
the posterior distributions of unknown variables given the model. In our example, we'll use
MCMC to obtain the samples.
The prototypical PyMC program has two components:
Deﬁne all variables, and how variables depend on each other
Run an algorithm to simulate a posterior distribution

Let's now obtain samples from the posterior. We select our prior as a Beta(11.5,48.5). Let's see
how observing 7 clicks from 10 impressions updates our beliefs:

Let's walk through each line of code:
with pm.Model() as model:
import pymc3 as pm
import numpy as np
#create our data:clicks = np.array([n_clicks])
#clicks represents our successes. We observed 7 clicks.impressions = np.array(
#this represents the number of trials. There were 10 impressions.
#sets a context; all code in block "belongs" to the model object
theta_prior = pm.Beta('prior', 11.5, 48.5)
#our prior distribution, Beta (11.5, 48.5)
observations = pm.Binomial('obs',n = impressions
, p = theta_prior
, observed = clicks) #Sampling distribition
#our prior p_prior will be updated with data
start = pm.find_MAP() #find good starting values for the sampling algor
#Max Aposterior values, or values that are most likely
step = pm.NUTS(state=start) #Choose a particular MCMC algorithm #w
trace = pm.sample(5000
, step
, start=start
, progressbar=True) #obtain samples
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pm.Model creates a PyMC model object. as model assigns it to the variable name "model", and
the with ... : syntax establishes a context manager. All PyMC objects created within the
context manager are added to the model object.
Theta_prior represents a random variable for click-through rates. It will serve as our prior
distribution for the parameter θ, the click-through rate of our facebook-yellow-dress campaign.
This random variable is generated from a beta distribution (pm.Beta); we name this random
variable "prior" and hardcode parameter values 11.5 and 48.5. We could have set the values of
these parameters as random variables as well, but we hardcode them here as they are known.
observations = pm.Binomial('obs',n = impressions , p = theta_prior
, observed = clicks)
This statement represents the likelihood of the data under the model. Again we deﬁne the
variable name and set parameter values with n and p. Note that for this variable, the parameter p
is assigned to a random variable, indicating that we are trying to model that variable. Lastly, we
provide observed instances of the variable (i.e. our data) with the observed keyword. Because
we have said this variable is observed, the model will not try to change its values.
start = pm.find_MAP()
step = pm.NUTS(state=start)
trace = pm.sample(2000, step, start=start, progressbar=True)
These three lines deﬁne how we are going to sample values from the posterior. pm.find_MAP()
will identify values of theta that are likely in the posterior, and will serve as the starting values for
our sampler.

pm.NUTS(state=start) will determine which sampler to use. The sampling algorithm deﬁnes
how we propose new samples given our current state. The proposals can be done completely
randomly, in which case we'll reject samples a lot, or we can propose samples more intelligently.
NUTS (short for the No-U-Turn sample) is an intelligent sampling algorithm. Other choices
include Metropolis Hastings, Gibbs, and Slice sampling.
Lastly, pm.sample(2000, step, start=start, progressbar=True) will generate samples for
us using the sampling algorithm and starting values deﬁned above.
Let's take the histogram of the samples obtained from PyMC to see what the most probable
values of θ are, compared with our prior distribution and the evidence (likelihood of our data for
each value of θ):
#plot the histogram of click through rates
plt.rcParams['figure.figsize'] = (16, 7)
#get histogram of samples from posterior distribution of CTRs
posterior_counts, posterior_bins = np.histogram(trace['prior']
,bins=zero_to_one)
#normalized histogramposterior_counts = posterior_counts / float(posterior_cou
#take the mean of the samples as most plausible value
most_plausible_theta = np.mean(trace['prior'])
#histogram of samples from prior distribution
prior_counts, bins = np.histogram(prior_samples
, zero_to_one)#normalize
prior_counts = map(lambda x: float(x)/prior_counts.sum()
, prior_counts)
#plot
ax.plot(bins[:-1],prior_counts, alpha = .2)
ax.plot(bins[:-1],posterior_counts)
ax.axvline(most_plausible_theta, linestyle = "--", alpha = .2)
line1, line2, line3, line4 = ax.lines
ax.legend((line1, line2, line3, line4), ('Evidence'
, 'Prior Probability for Theta'
, 'Posterior Probability for Theta'
, 'Most Plausible Theta'
), loc = 'upper left')
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Now that we have a full distribution for the probability of various values of θ, we can take the
mean of the distribution as our most plausible value for θ, which is about 0.27.
The data has caused us to believe that the true click-through rate is higher than we originally
thought, but far lower than the 0.7 click-through rate observed so far from the facebook-yellow-
dress campaign. Why is this the case? Note how wide our likelihood function is; it's telling us that
there is a wide range of values of θ under which our data is likely. If the range of values under
which the data were plausible were narrower, then our posterior would have shifted further. See
what happens to the posterior if we observed a 0.7 click-through rate from 10, 100, 1,000, and
10,000 impressions:
ax.grid()
ax.set_title("Prior Distribution Updated with Some Evidence")
plt.show()
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import pymc3 as pm
import numpy as np
#create our data:
traces = {}
for ad_impressions in [10, 100, 1000, 10000]: #maintaining observed CTR of 0.7
clicks = np.array([ctr * ad_impressions]) #re-estimate the posterior fo
impressions = np.array([ad_impressions]) #increasing numbers of impress
observations = pm.Binomial('obs',n = impressions
, p = theta_prior
, observed = clicks)
start = pm.find_MAP()
step = pm.NUTS(state=start)
trace = pm.sample(5000
, step
, start=start
, progressbar=True)
traces[ad_impressions] = trace
ax.plot(bins[:-1],prior_counts, alpha = .2)
counts = {}
for ad_impressions in [10, 100, 1000, 10000]:
trace = traces[ad_impressions]
posterior_counts, posterior_bins = np.histogram(trace['prior'], bins=[j/10
posterior_counts = posterior_counts / float(len(trace))
ax.plot(bins[:-1], posterior_counts)
line0, line1, line2, line3, line4 = ax.lines
ax.legend((line0, line1, line2, line3, line4), ('Prior Distribution'
,'Posterior after 10 Impressio
, 'Posterior after 100 Impress
, 'Posterior after 1000 Impres
,'Posterior after 10000 Impres
ax.axvline(ctr, linestyle = "--", alpha = .5)
ax.grid()
ax.set_ylabel("Probability of Theta")
ax.set_title("Posterior Shifts as Weight of Evidence Increases")
plt.show()
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As we obtain more and more data, we are more certain that the 0.7 success rate is the true
success rate. Conditioning on more data as we update our prior, the likelihood function begins
to play a larger role in our ultimate assessment because the weight of the evidence gets
stronger. This would be particularly useful in practice if we wanted a continuous, fair assessment
of how our campaigns are performing without having to worry about overﬁtting to a small
sample.
There are a lot of concepts are beyond the scope of this tutorial, but are important for doing
Bayesian analysis successfully, such as how to choose a prior, which sampling algorithm to
choose, determining if the sampler is giving us good samplers, or checking for sampler
convergence. Hopefully this tutorial inspires you to continue exploring the fascinating world of
Bayesian inference.
Additional Information
Books:

Bayesian Data Analysis by Andrew Gelman
The Bayesian Choice by Christian P. Robert
Jaynes' Probability Theory
Software:
PyMC
Stan
Dimple
Figaro
Hakaru
Papers:
Overview of MCMC
Historical Discussion of Bayesian Probability
Other:
Bayesian Methods for Hackers
Want to keep learning? Download our new study from Forrester about the tools and
practices keeping companies on the forefront of data science.

Photo by mattbuck. [CC BY-SA 3.0], via Wikimedia Commons

  
AARON KRAMER
Data analyst at DataScience. I'm into basketball, python, machine learning,
algorithms and economics.
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