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A primer in Bayesian thinking and AB testing using Pyro
This article is an introduction to AB testing using the Python probability programming language (PPL) Pyro, an alternative to PyMC. The motivation for writing this article was to further my understanding of Bayesian statistical inference using the Pyro framework and to help others in the process. As such, feedback is welcomed and encouraged.
Introduction
My previous experience with Bayesian modelling in Python was with PyMC. However, I have found it troublesome to work with some of the latest versions. My research into other probabilistic programming languages led me to discover Pyro, a universal PPL built by Uber and supported by PyTorch on the backend. The documentation for both Pyro and PyTorch is linked below.
Whilst exploring Pyro, I found it difficult to find end-to-end tutorials for AB testing using the package. This article aims to fill that gap.
This article has five sections. In the first section, I will give a primer on Bayesian thinking, a background in the philosophy that the methodology speaks for. I will give a brief technical background on Pyro and the Bayesian methods used to make our statistical inferences. Next, I will perform an AB test using Pyro and discuss the results. I will then explain the case for Bayesian AB testing in a business setting. The final section will summarise.
A Primer in Bayesian Thinking
The Bayesian process is relatively simple at a high level. First, you have a variable that you are interested in. We state our current understanding of that variable, which we express as a probability distribution (everything in Bayes’ world is a probability distribution). This is called a prior. Probability in Bayesian inference is epistemic, meaning it arises through our degree of knowledge. Thus, the probability distribution we state as our prior is as much of a statement of uncertainty, as it is understanding. We then observe events from the real world. These observations are then used to update our understanding of the variable we are interested in. The new state of our understanding is called the posterior. We also characterise the posterior with a probability distribution, the probability of the variable we are interested in, given the data we have observed. This process is illustrated in the flow diagram below, where theta is the variable we are interested in and data is the outcome of the events we have observed.
The Bayesian process is actually cyclical, because we then repeat this process, starting again but using our new-found knowledge after observing the world. Our old posterior becomes our new prior, we observe new events and once again update our understanding, becoming ‘less and less and less wrong’ as Nate Silver put it in his book The Signal and the Noise. We continuously reduce our uncertainty concerning the variable, converging towards a state of certainty (but we can never be certain). Mathematically, this way of thinking is encapsulated by Bayes’ theorem.
In practice, Bayes’ theorem quickly becomes computationally intractable for large models across higher dimensions. There are numerous approaches to solve this issue, but the method we will use today is called Markov Chain Monte Carlo, or MCMC. MCMC is a class of algorithms (we will be using one called Hamiltonian Monte Carlo), which draws samples from a probability distribution intelligently. It is beyond the scope of this article to dive deep into this, but I will provide some helpful references at the end for further reading. For now, it is sufficient to know that Bayes’ theorem is too complex to be able to calculate, so we leverage the power of advanced algorithms, such as MCMC to help. This article will focus on MCMC using Pyro. However, Pyro does emphasise the use of Stochastic Variational Inference (SVI), an approximation-based approach, which will not be covered here.
AB Testing Using Pyro
Consider a company that has designed a new website landing page and wants to understand the impact this will have on conversion, i.e. do visitors continue their web session on the website after landing on the page? In test group A, website visitors will be shown the current landing page. In test group B, website visitors will be shown the new landing page. In the rest of the article, I will refer to test group A as the control group, and group B as the treatment group. The business is sceptical about the change and has opted for an 80/20 split in session traffic. The total number of visitors and the total number of page conversions for each test group are summarised below.
The null hypothesis of the AB test is that there will be no change in page conversion for the two test groups. Under the frequentist framework, this would be expressed as the following for a two-sided test, where r_c and r_t are the page conversion rates in the control and treatment groups, respectively.
A significance test would then seek to either reject or fail to reject the null hypothesis. Under the Bayesian framework, we express the null hypothesis slightly differently by asserting the same prior for each of the test groups.
Let’s pause and outline exactly what is happening during our test. The variable we are interested in is the page conversion rate. This is simply calculated by taking the number of distinct converted visitors over the total number of visitors. The event that generates this rate is whether the visitor clicks through the page. There are only two possible outcomes here for each visitor, either the visitor clicks through the page and converts, or does not. Some of you might recognise that for each distinct visitor, this is an example of a Bernoulli trial; there is one trial and two possible outcomes. Now, when we collect a set of these Bernoulli trials, we have a binomial distribution. When the random variable X has a binomial distribution, we give it the following notation:
Where n is the number of visitors (or the number of Bernoulli trials), and p is the probability of the event on each trial. p is what we are interested in here, we want to understand what the probability of a visitor converting on the page is in each test group. We have observed some data, but as mentioned in the previous section, we first need to define our prior. As always in Bayesian statistics, we need to define this prior as a probability distribution. As mentioned before, this probability distribution is a characterisation of our uncertainty. Beta distributions are commonly used for modelling probabilities, as it is defined between the intervals of [0,1]. Furthermore, using a beta distribution as our prior for a binomial likelihood function gives us the helpful property of conjugacy, which means our posterior will be generated from the same distribution as our prior. We say that the beta distribution is a conjugate prior. A beta distribution is defined by two parameters, alpha, and confusingly, beta.
With access to historical data, we can assert an informed prior. We do not necessarily need historical data, we could use our intuition to inform our understanding, but for now let’s assume we have neither (later in this tutorial we will use informed priors, but to demonstrate the impact, I will start with the uninformed). Let’s assume we have no understanding of the conversion rate on the company’s site, and therefore define our prior as Beta(1,1). This is called a flat prior. The probability distribution of this function looks like the graph below, the same as a uniform distribution defined between the intervals [0,1]. By asserting a Beta(1,1) prior, we say that all possible values of the page conversion rate are equally probable.
We now have all the information we need, the priors, and the data. Let’s jump into the code. The code provided herein will provide a framework to get started with AB testing using Pyro; it therefore neglects some features of the package. To help optimise your code further and take full advantage of Pyro’s capabilities, I recommend referring to the official documentation.
First, we need to import our packages. The final line is good practice, particularly when working in notebooks, clearing the store of parameters we have built up.
import pyro
import pyro.distributions as dist
from pyro.infer import NUTS, MCMC
import torch
from torch import tensor
import matplotlib.pyplot as plt
import seaborn as sns
from functools import partial
import pandas as pd
pyro.clear_param_store()
Models in Pyro are defined as regular Python functions. This is helpful as it makes it intuitive to follow.
def model(beta_alpha, beta_beta):
def _model_(traffic: tensor, number_of_conversions: tensor):
# Define Stochastic Primatives
prior_c = pyro.sample('prior_c', dist.Beta(beta_alpha, beta_beta))
prior_t = pyro.sample('prior_t', dist.Beta(beta_alpha, beta_beta))
priors = torch.stack([prior_c, prior_t])
# Define the Observed Stochastic Primatives
with pyro.plate('data'):
observations = pyro.sample('obs', dist.Binomial(traffic, priors),
obs = number_of_conversions)
return partial(_model_)
A few things to break down and explain here. First, we have a function wrapped inside an outer function, the outer function returns the partial function of the inner function. This allows us to change our priors, without needing to change the code. I have referred to the variables defined in the inner function as primitives, think of primitives as variables in the model. We have two types of primitives in the model, stochastic and observed stochastic. In Pyro, we do not have to explicitly define the difference, we simply add the obs argument to the sample method when it is an observed primitive and Pyro interprets it accordingly. Observed primitives are contained within the context manager pyro.plate(), which is best practice and makes our code look cleaner. Our stochastic primitives are our two priors, characterised by Beta distributions, governed by the alpha and beta parameters that we pass in from the outer function. As previously mentioned, we assert the null hypothesis by defining these as equal. We then stack these two primitives together using tensor.stack(), which performs an operation akin to concatenating a Numpy array. This will return a tensor, the data structure required for inference in Pyro. We have defined our model, now let’s move onto the inference stage.
As previously mentioned, this tutorial will use MCMC. The function below will take the model that we have defined above and the number of samples we wish to use to generate our posterior distribution as a parameter. We also pass our data into the function, as we did for the model.
def run_infernce(model, number_of_samples, traffic, number_of_conversions):
kernel = NUTS(model)
mcmc = MCMC(kernel, num_samples = number_of_samples, warmup_steps = 200)
mcmc.run(traffic, number_of_conversions)
return mcmc
The first line inside this function defines our kernel. We use the NUTS class to define our kernel, which stands for No-U-Turn Sampler, an autotuning version of Hamiltonian Monte Carlo. This tells Pyro how to sample from the posterior probability space. Again, it is beyond the scope of this article to dive deeper into this topic, but for now, it is sufficient to know that NUTS allows us to sample from the probability space intelligently. The kernel is then used to initialise the MCMC class on the second line, specifying it to use NUTS. We pass the number_of_samples argument in the MCMC class which is the number of samples used to generate the posterior distribution. We assign the initialised MCMC class to the mcmc variable and call the run() method, passing our data as parameters. The function returns the mcmc variable.
This is all we need; the following code defines our data and calls the functions we have just made using the Beta(1,1) prior.
traffic = torch.tensor([5523., 1379.])
conversions =torch.tensor([2926., 759.])
inference = run_infernce(model(1,1), number_of_samples = 1000,
traffic = traffic, number_of_conversions = conversions)
The first element of the traffic and conversions tensors are the counts for the control group, and the second element in each tensor is the counts for the treatment group. We pass the model function, with the parameters to govern our prior distribution, alongside the tensors we have defined. Running this code will generate our posterior samples. We run the following code to extract the posterior samples and pass them to a Pandas dataframe.
posterior_samples = inference.get_samples()
posterior_samples_df = pd.DataFrame(posterior_samples)
Notice the column names of this dataframe are the strings we passed when we defined our primitives in the model function. Each row in our dataframe contains samples drawn from the posterior distribution, and each of these samples represents an estimate of the page conversion rate, the probability value p that governs our Binomial distribution. Now we have returned the samples, we can plot our posterior distributions.
Results
An insightful way to visualise the results of the AB test with two test groups is by a joint kernel density plot. It allows us to visualise the density of samples in the probability space across both distributions. The graph below can be produced from the dataframe we have just built.
The probability space contained in the graph above can be divided across its diagonal, anything above the line would indicate regions where the estimation of the conversion rate is higher in the treatment group than the control and vice versa. As illustrated in the plot, the samples drawn from the posterior are densely populated in the region which would indicate the conversion rate is higher in the treatment group. It is important to highlight that the posterior distribution for the treatment group is wider than the control group, reflecting a higher degree of uncertainty. This is a result of observing less data in the treatment group. Nevertheless, the plot strongly indicates that the treatment group has outperformed the control group. By collecting an array of samples from the posterior and taking the element-wise difference, we can say that the probability that the treatment group outperforms the control group is 90.4%. This figure suggests that 90.4% of the samples drawn from the posterior will be populated above the diagonal in the joint density plot above.
These results were achieved by using a flat (uninformed) prior. The use of an informed prior may help improve the model, particularly when the availability of observed data is limited. A helpful exercise is to explore the effects of using different priors. The plot below shows the Beta(2,2) probability density function and the joint plot it produces when we rerun the model. We can see that using the Beta(2,2) prior produces a very similar posterior distribution for both test groups.
The samples drawn from the posterior suggest there is a 91.5% probability that the treatment group performs better than the control. Therefore, we do believe with a higher degree of certainty that the treatment group is better than the control versus using a flat prior. However, in this example the difference is negligible.
There is one other thing I would like to highlight about these results. When we ran the inference, we told Pyro to generate 1000 samples from the posterior. This is an arbitrary number, selecting a different number of samples can change the results. To highlight the effect of increasing the number of samples, I ran an AB test where the observations from the control and treatment groups were the same, each with an overall conversion rate of 50%. Using a Beta(2,2) prior generates the following posterior distributions as we incrementally increase the number of samples.
When we run our inference with just 10 samples, the posterior distribution for the control and treatment groups are relatively wide and adopt different shapes. As the number of samples that we draw increases, the distributions converge, eventually generating nearly identical distributions. Furthermore, we observe two properties of statistical distributions, the central limit theorem and the law of large numbers. The central limit theorem states that the distribution of sample means converges towards a normal distribution as the number of samples increases, and we can see that in the plot above. Additionally, the law of large numbers states that as the sample size grows, the sample mean converges towards the population mean. We can see that the mean of the distributions in the bottom right tile is approximately 0.5, the conversion rate observed in each of the test samples.
The Business Case for Bayesian AB Testing
Bayesian AB testing can help elevate a business’s test and learn culture. Bayesian statistical inference allows for small uplifts in the test to be detected quickly as it is not reliant on long-run probabilities to draw conclusions. Test conclusions can be reached faster and therefore the rate of learning increases. Bayesian AB testing also allows for early stoppage of a test, if results gained through ‘peeking’ indicate test groups are performing significantly worse than the control then the test can be stopped. Therefore, the opportunity cost of testing can be significantly reduced. This is a major benefit of Bayesian AB testing; results can be constantly monitored, and our posteriors constantly updated. Conversely, the early detection of an uplift in the test subject can help businesses implement changes faster, reducing the latency of implementing revenue-improving changes. Customer-facing businesses must be able to quickly implement and analyse test results, which is facilitated by the Bayesian AB testing framework.
Summary
This article has given a brief background on Bayesian thinking and explored the results of Bayesian AB testing using Pyro. I hope you have found this article insightful. As mentioned in the introduction, feedback is welcomed and encouraged. As promised, I have linked some further reading material below.
Recommended Material
The following books provide good insight into Bayesian Inference:
- The Signal and the Noise: The Art and Science of Prediction — Nate Silver
- The Book of Why: The New Science of Cause and Effect — Judea Pearl and Dana Mackenzie. Although this book largely focuses on causality, chapter 3 is a worthwhile read on Bayes’.
- Bayesian Methods for Hackers: Probabilistic Programming and Bayesian Inference — Cameron Davidson-Pilon. This book is also available on Git, I have linked it below.
These Medium articles provide detailed explanations of MCMC.
- Monte Carlo Markov Chain (MCMC) explained
- Bayesian inference problem, MCMC and variational inference
Bayesian AB Testing with Pyro was originally published in Towards Data Science on Medium, where people are continuing the conversation by highlighting and responding to this story.
Originally appeared here:
Bayesian AB Testing with Pyro
