Single parameter inference

In the last two sections, we have learned several important concepts, but two of them are essentially the core of Bayesian statistics, so let's restate them in a single sentence. Probabilities are used to measure the uncertainty we have about parameters, and Bayes' theorem is the mechanism to correctly update those probabilities in the light of new data, hopefully reducing our uncertainty.

Now that we know what Bayesian statistics is, let's learn how to do Bayesian statistics with a simple example. We are going to begin inferring a single unknown parameter.

The coin-flipping problem

The coin-flip problem is a classical problem in statistics and goes like this. We toss a coin a number of times and record how many heads and tails we get. Based on this data we try to answer questions such as is the coin fair? Or, more generally, how biased is the coin? While this problem may sound dull, we should not underestimate it. The coin-flipping problem is a great example to learn the basic of Bayesian statistics; on the one hand, it is about tossing coins, something familiar to almost anyone; on the other, it is a simple model that we can solve and compute with ease. Besides, many real problems consist of binary mutually exclusive outcomes such as 0 or 1, positive or negative, odds or evens, spam or ham, safe or unsafe, healthy or unhealthy, and so on. Thus, even when we are talking about coins, this model applies to any of those problems.

In order to estimate the bias of a coin, and in general to answer any questions in a Bayesian setting, we will need data and a probabilistic model. For this example, we will assume that we have already tossed a coin a number of times and we have recorded the number of observed heads, so the data part is done. Getting the model will take a little bit more effort. Since this is our first model, we will do all the necessary math (don't be afraid, I promise it will be painless) and we will proceed step by step very slowly. In the next chapter we will revisit this problem by using PyMC3 to solve it numerically, that is, without us doing the math. Instead we will let PyMC3 and our computer do the math.

The general model

The first thing we will do is generalize the concept of bias. We will say that a coin with a bias of 1 will always land heads, one with a bias of 0 will always land tails, and one with a bias of 0.5 will land half of the time heads and half of the time tails. To represent the bias, we will use the parameter , and to represent the total number of heads for an N number of tosses, we will use the variable y. According to Bayes' theorem we have the following formula:

Notice that we need to specify which prior and likelihood we will use. Let's start with the likelihood.

Choosing the likelihood

Let's assume that a coin toss does not affect other tosses, that is, we are assuming coin tosses are independent of each other. Let's also assume that only two outcomes are possible, heads or tails. I hope you agree these are very reasonable assumptions to make for our problem. Given these assumptions, a good candidate for the likelihood is the binomial distribution:

This is a discrete distribution returning the probability of getting y heads (or in general, success) out of N coin tosses (or in general, trials or experiments) given a fixed value of . The following code generates 9 binomial distributions; each subplot has its own legend indicating the corresponding parameters:

n_params = [1, 2, 4]
p_params = [0.25, 0.5, 0.75]
x = np.arange(0, max(n_params)+1)
f, ax = plt.subplots(len(n_params), len(p_params), sharex=True, 
  sharey=True)
for i in range(3):
    for j in range(3):
        n = n_params[i]
        p = p_params[j]
        y = stats.binom(n=n, p=p).pmf(x)
        ax[i,j].vlines(x, 0, y, colors='b', lw=5)
        ax[i,j].set_ylim(0, 1)
        ax[i,j].plot(0, 0, label="n = {:3.2f}\np = {:3.2f}".format(n, p), alpha=0)
        ax[i,j].legend(fontsize=12)
ax[2,1].set_xlabel('$\\theta$', fontsize=14)
ax[1,0].set_ylabel('$p(y|\\theta)$', fontsize=14)
ax[0,0].set_xticks(x)

The binomial distribution is also a reasonable choice for the likelihood. Intuitively, we can see that indicates how likely it is that we will obtain a head when tossing a coin, and we have observed that event y times. Following the same line of reasoning we get that is the chance of getting a tail, and that event has occurred N-y times.

OK, so if we know , the binomial distribution will tell us the expected distribution of heads. The only problem is that we do not know ! But do not despair; in Bayesian statistics, every time we do not know the value of a parameter, we put a prior on it, so let's move on and choose a prior.

Choosing the prior

As a prior we will use a beta distribution, which is a very common distribution in Bayesian statistics and looks like this:

If we look carefully we will see that the beta distribution looks similar to the binomial except for the term with the . This is the Greek uppercase gamma letter and represents what is known as gamma function. All that we care about at this point is that the first term is a normalization constant that ensures the distribution integrates to 1 and that the beta distribution has two parameters, and , that control the distribution. Using the following code, we will explore our third distribution so far:

params = [0.5, 1, 2, 3]
x = np.linspace(0, 1, 100)
f, ax = plt.subplots(len(params), len(params), sharex=True, 
  sharey=True)
for i in range(4):
    for j in range(4):
        a = params[i]
        b = params[j]
        y = stats.beta(a, b).pdf(x)
        ax[i,j].plot(x, y)
        ax[i,j].plot(0, 0, label="$\\alpha$ = {:3.2f}\n$\\beta$ = {:3.2f}".format(a, b), alpha=0)
        ax[i,j].legend(fontsize=12)
ax[3,0].set_xlabel('$\\theta$', fontsize=14)
ax[0,0].set_ylabel('$p(\\theta)$', fontsize=14)

OK, the beta distribution is nice, but why are we using it for our model? There are many reasons to use a beta distribution for this and other problems. One of them is that the beta distribution is restricted to be between 0 and 1, in the same way our parameter is. Another reason is its versatility. As we can see in the preceding figure, the distribution adopts several shapes, including a uniform distribution, Gaussian-like distributions, U-like distributions, and so on. A third reason is that the beta distribution is the conjugate prior of the binomial distribution (which we are using as the likelihood). A conjugate prior of a likelihood is a prior that, when used in combination with the given likelihood, returns a posterior with the same functional form as the prior. Untwisting the tongue, every time we use a beta distribution as prior and a binomial distribution as likelihood, we will get a beta as a posterior. There are other pairs of conjugate priors, for example, the Gaussian distribution is the conjugate prior of itself. For a more detailed discussion read https://en.wikipedia.org/wiki/Conjugate_prior. For many years, Bayesian analysis was restricted to the use of conjugate priors. Conjugacy ensures mathematical tractability of the posterior, which is important given that a common problem in Bayesian statistics is to end up with a posterior we cannot solve analytically. This was a deal breaker before the development of suitable computational methods to solve any possible posterior. From the next chapter on, we will learn how to use modern computational methods to solve Bayesian problems whether we choose conjugate priors or not.

Getting the posterior

Let's remember Bayes' theorem says that the posterior is proportional to the likelihood times the prior:

So for our problem, we have to multiply the binomial and the beta distributions:

Now let's simplify this expression. To our practical concerns we can drop all the terms that do not depend on and our results will still be valid. So we can write the following:

Reordering it, we get the following:

If we pay attention, we will see that this expression has the same functional form of a beta distribution (except for the normalization) with and , which means that the posterior for our problem is the beta distribution:

Computing and plotting the posterior

Now that we have the analytical expression for the posterior, let's use Python to compute it and plot the results. In the following code you will see there is actually one line that computes the results while the others are there just to plot them:

theta_real = 0.35
trials = [0, 1, 2, 3, 4, 8, 16, 32, 50, 150]
data = [0, 1, 1, 1, 1, 4, 6, 9, 13, 48]

beta_params = [(1, 1), (0.5, 0.5), (20, 20)]
dist = stats.beta
x = np.linspace(0, 1, 100)

for idx, N in enumerate(trials):
    if idx == 0:
        plt.subplot(4,3, 2)
    else:
        plt.subplot(4,3, idx+3)
    y = data[idx]
    for (a_prior, b_prior), c in zip(beta_params, ('b', 'r', 'g')):
        p_theta_given_y = dist.pdf(x, a_prior + y, b_prior + N - y)
        plt.plot(x, p_theta_given_y, c)
        plt.fill_between(x, 0, p_theta_given_y, color=c, alpha=0.6)

    plt.axvline(theta_real, ymax=0.3, color='k')
    plt.plot(0, 0, label="{:d} experiments\n{:d} heads".format(N, y), alpha=0)
    plt.xlim(0,1)
    plt.ylim(0,12)
    plt.xlabel(r'$\theta$') 
    plt.legend()
    plt.gca().axes.get_yaxis().set_visible(False)
plt.tight_layout()

On the first line we have 0 experiments done, hence these curves are just our priors. We have three curves, one per prior:

• The blue one is a uniform prior. This is equivalent to saying that all the possible values for the bias are equally probable a priori.
• The red one is similar to the uniform. For the sake of this example we will just say that we are a little bit more confident that the bias is either 0 or 1 than the rest of the values.
• The green and last one is centered and concentrated around 0.5, so this prior is compatible with information indicating that the coin has more or less about the same chance of landing heads or tails. We could also say this prior is compatible with the belief that most coins are fair. While such a word is commonly used in Bayesian discussions we think is better to talk about models that are informed by data.

The rest of the subplots show posteriors for successive experiments. Remember that we can think of posteriors as updated priors given the data. The number of experiments (or coin tosses) and the number of heads are indicated in each subplot's legend. There is also a black vertical line at 0.35 representing the true value for . Of course, in real problems we do not know this value, and it is here just for pedagogical reasons. This figure can teach us a lot about Bayesian analysis, so let's take a moment to understand it:

• The result of a Bayesian analysis is the posterior distribution, not a single value but a distribution of plausible values given the data and our model.
• The most probable value is given by the mode of the posterior (the peak of the distribution).
• The spread of the posterior is proportional to the uncertainty about the value of a parameter; the more spread the distribution, the less certain we are.
• Even when it is easy to see that the uncertainty we have in the first example is larger than in the second one because we have more data that supports our inference. This intuition is reflected in the posterior.
• Given a sufficiently large amount of data, two or more Bayesian models with different priors will tend to converge to the same result. In the limit of infinite data, no matter which prior we use, we will always get the same posterior. Remember that infinite is a limit and not a number, so from a practical point of view in some cases the infinite amount of data could be approximated with a really small number of data points.
• How fast posteriors converge to the same distribution depends on the data and the model. In the previous figure we can see that the blue and red posteriors look almost indistinguishable after only 8 experiments, while the red curve continues to be separated from the other two even after 150 experiments.
• Something not obvious from the figure is that we will get the same result if we update the posterior sequentially than if we do it all at once. We can compute the posterior 150 times, each time adding one more observation and using the obtained posterior as the new prior, or we can just compute one posterior for the 150 tosses at once. The result will be exactly the same. This feature not only makes perfect sense, also leads to a natural way of updating our estimations when we get new data, a situation common in many data analysis problems.

Influence of the prior and how to choose one

From the preceding example, it is clear that priors influence the result of the analysis. This is totally fine, priors are supposed to do this. Newcomers to Bayesian analysis (as well as detractors of this paradigm) are in general a little nervous about how to choose priors, because they do not want the prior to act as a censor that does not let the data speak for itself! That's okay, but we have to remember that data does not really speak; at best, data murmurs. Data only makes sense in the light of our models, including mathematical and mental models. There are plenty of examples in the history of science where the same data leads people to think differently about the same topics. Check for example a recent experiment that appeared in the New York Times http://www.nytimes.com/interactive/2016/09/20/upshot/the-error-the-polling-world-rarely-talks-about.html?_r=0.

Some people fancy the idea of using non-informative priors (also known as flat, vague, or diffuse priors); these priors have the least possible amount of impact on the analysis. While it is possible to use them, in general, we can do better. Throughout this book we will follow the recommendations of Gelman, McElreath, Kruschke and many others, and we will prefer weakly informative priors. For many problems we often know something about the values a parameter can take, we may know that a parameter is restricted to being positive, or we may know the approximate range it can take, or if we expect the value to be close to zero or above/below some value. In such cases, we can use priors to put some weak information in our models without being afraid of being too pushy with our data. Because these priors work to keep the posterior distribution approximately within certain reasonable bounds, they are also know as regularizing priors.

Of course, it can also be possible to use informative priors. These are very strong priors that convey a lot of information. Depending on your problem, it could be easy or not to find this type of prior; for example, in my field of work (structural bioinformatics), people have been using all the prior information they can get, in Bayesian and non-Bayesian ways, to study and especially predict the structure of proteins. This is reasonable because we have been collecting data from thousands of carefully designed experiments for decades and hence we have a great amount of trustworthy prior information at our disposal. Not using it would be absurd! So the take-home message is if you have reliable prior information, there is no reason to discard that information, including the non-nonsensical argument that not using information we trust is objective. Imagine if every time an automotive engineer has to design a new car, she has to start from scratch and re-invent the combustion engine, the wheel, and for that matter, the whole concept of a car. That is not the way things work.

Now we know that there are different kind of priors, but this probably doesn't make us less nervous about choosing among them. Maybe it would be better to not have priors at all. That would make things easier. Well, every model, Bayesian or not has some kind of priors in some way or another, even if the prior does not appear explicitly. In fact many results from frequentist statistics can be seen as special cases of a Bayesian model under certain circumstances, such as flat priors. Let's pay attention to the previous figure one more time. We can see that the mode (the peak of the posterior) of the blue posterior agrees with the expected value for from a frequentist analysis:

Notice that is a point estimate (a number) and not a posterior distribution (or any other type of distribution for that matter). So notice that you can not really avoid priors, but if you include them in your analysis you will get a distribution of plausible values and not only the most probable one. Another advantage of being explicit about priors is that we get more transparent models, meaning more easy to criticize, debug (in a broad sense of the word), and hopefully improve. Building models is an iterative process; sometimes the iteration takes a few minutes, sometimes it could take years. Sometimes it will only involve you and sometimes people you do not even know. Reproducibility matters and transparent assumptions in a model contributes to it.

We are free to use more than one prior (or likelihood) for a given analysis if we are not sure about any special one. Part of the modeling process is about questioning assumptions, and priors are just that. Different assumptions will lead to different models, using data and our domain knowledge of the problem we will be able to compare models. Chapter 06, Model Comparison will be devoted to this issue.

Since priors have a central role in Bayesian statistics, we will keep discussing them as we face new problems. So if you have doubts and feel a little bit confused about this discussion just keep calm and don't worry, people have been confused for decades and the discussion is still going on.

Communicating a Bayesian analysis

Now that we have the posterior, the analysis is finished and we can go home. Well, not yet! We probably need to communicate or summarize the results to others, or even record for later use by ourselves.

Model notation and visualization

If you want to communicate the result, you may need, depending on your audience, to also communicate the model. A common notation to succinctly represent probabilistic models is as follows:

• θ ∼ Beta(α, β)
• y ∼ Bin(n = 1, p = θ)

This is the model we use for the coin-flip example. As we may remember, the symbol ~ indicates that the variable is a random variable distributed according to the distribution on the right, that is, is distributed as a beta distribution with parameters and , and y is distributed as a binomial with parameter n=1 and . The very same model can be represented graphically using Kruschke's diagrams:

On the first level, we have the prior that generates the values for , then the likelihood and, on the last line, the data. Arrows indicate the relationship between variables, and the ~ symbol indicates the stochastic nature of the variables.

All Kruschke's diagrams in the book were made using the templates provided by Rasmus Bååth (http://www.sumsar.net/blog/2013/10/diy-kruschke-style-diagrams/). I would like to specially thanks him for making these templates available.

Summarizing the posterior

The result of a Bayesian analysis is the posterior distribution. This contains all the information about our parameters according to the data and the model. If possible, we can just show the posterior distribution to our audience. In general, it is also a good idea to report the mean (or mode or median) of the distribution to have an idea of the location of the distribution and some measure, such as the standard deviation, to have an idea of the dispersion and hence the uncertainty in our estimate. The standard deviation works well for normal-like distributions but can be misleading for other types of distributions, such as skewed ones. So intead, we could use the following approach.

Highest posterior density

A commonly used device to summarize the spread of a posterior distribution is to use a Highest Posterior Density (HPD) interval. An HPD is the shortest interval containing a given portion of the probability density. One of the most commonly used is the 95% HPD or 98% HPD, often accompanied by the 50% HPD. If we say that the 95% HPD for some analysis is [2-5], we mean that according to our data and model we think the parameter in question is between 2 and 5 with a 0.95 probability. This is a very intuitive interpretation, to the point that often people misinterpret frequentist confidence intervals as if they were Bayesian credible intervals. If you are familiar with the frequentist paradigm please note that both type of intervals have different interpretations. Performing a fully Bayesian analysis enables us to talk about the probability of a parameter having some value. While this is not possible in the frequentist framework since parameters are fixed by design, a frequentist confidence interval contains or does not contain the true value of a parameter. Another word of caution before we continue: there is nothing special about choosing 95% or 50% or any other value. They are just arbitrary commonly used values; we are free to choose the 91.37% HPD interval if we like. If you want to use the 95% value, it's OK; just remember that this is just a default value and any justification of which value we should use will be always context-dependent and not automatic.

Computing the 95% HPD for a unimodal distribution is easy, since it is defined by the percentiles 2.5 and 97.5:

def naive_hpd(post):
    sns.kdeplot(post)
    HPD = np.percentile(post, [2.5, 97.5])
    plt.plot(HPD, [0, 0], label='HPD {:.2f} {:.2f}'.format(*HPD), 
      linewidth=8, color='k')
    plt.legend(fontsize=16);
    plt.xlabel(r'$\theta$', fontsize=14)
    plt.gca().axes.get_yaxis().set_ticks([])

    
np.random.seed(1)
post = stats.beta.rvs(5, 11, size=1000)
naive_hpd(post)
plt.xlim(0, 1)

For a multi-modal distribution, the computation of the HPD is a little bit more complicated. If we apply our naive definition of the HPD to a mixture of Gaussians we will get the following:

np.random.seed(1)    
gauss_a = stats.norm.rvs(loc=4, scale=0.9, size=3000)
gauss_b = stats.norm.rvs(loc=-2, scale=1, size=2000)
mix_norm = np.concatenate((gauss_a, gauss_b))

naive_hpd(mix_norm)

As we can see in the preceding figure, the HPD computed in the naive way includes values with a low probability, approximately between [0, 2]. To compute the HPD in the correct way we will use the function plot_post, which you can download from the accompanying code that comes with the book:

from plot_post import plot_post
plot_post(mix_norm, roundto=2, alpha=0.05)
plt.legend(loc=0, fontsize=16)
plt.xlabel(r"$\theta$", fontsize=14)

As you can see from the preceding figure, the 95% HPD is composed of two intervals. plot_post also returns the values for the two modes.