Density and Likelihood¶

Here’s a question from the Reddit statistics forum.

I’m a math graduate and am partially self taught. I am really frustrated with likelihood and probability density, two concepts that I personally think are explained so disastrously that I’ve been struggling with them for an embarrassingly long time. Here’s my current understanding and what I want to understand:

• probability density is the ‘concentration of probability’ or probability per unit and the value of the density in any particular interval depends on the density function used. When you integrate the density curve over all outcomes x in X where X is a random variable and x are its realizations then the result should be all the probability or 1.

• likelihood is the joint probability, in the discrete case, of observing fixed and known data depending on what parameter(s) value we choose. In the continuous case we do not have a nonzero probability of any single value but we do have nonzero probability within some infinitely small interval (containing infinite values?) [x, x+h] and maximizing the likelihood of observing this data is equivalent to maximizing the probability of observing it, which we can do by maximizing the density at x.

My questions are:

Is what I wrote above correct? Probability density and likelihood are not the same thing. But what the precise distinction is in the continuous case is not completely cut and dry to me. […]

I agree with OP — these topics are confusing and not always explained well. So let’s see what we can do.

Mass¶

I’ll start with a discrete distribution, so we can leave density out of it for now and focus on the difference between a probability mass function (PMF) and a likelihood function.

As an example, suppose we know that a hockey team scores goals at a rate of 3 goals per game on average. If we model goal scoring as a Poisson process — which is not a bad model — the number of goals per game follows a Poisson distribution with parameter mu=3.

The PMF of the Poisson distribution tells us the probability of scoring k goals in a game, for non-negative values of k.

Here’s what it looks like.

The PMF is a function of k, with mu as a fixed parameter.

The values in the distribution are probability masses, so if we want to know the probability of scoring exactly 5 goals, we can look it up like this.

It’s about 10%.

The sum of the ps is close to 1.

If we extend the ks to infinity, the sum is exactly 1. So this set of probability masses is a proper discrete distribution.

Likelihood¶

Now suppose we don’t know the goal scoring rate, but we observe 4 goals in one game. There are several ways we can use this data to estimate mu. One is to find the maximum likelihood estimator (MLE), which is the value of mu that makes the observed data most likely.

To find the MLE, we need to maximize the likelihood function, which is a function of mu with a fixed number of observed goals, k. To evaluate the likelihood function, we can use the PMF of the Poisson distribution again, this time with a single value of k and a range of values for mu.

Here’s what the likelihood function looks like.

To find the value of mu that maximizes the likelihood of the data, we can use argmax to find the index of the highest value in ls, and then look up the corresponding element of mus.

In this case, the maximum likelihood estimator is equal to the number of goals we observed.

That’s the answer to the estimation problem, but now let’s look more closely at those likelihoods. Here’s the likelihood at the maximum of the likelihood function.

This likelihood is a probability mass — specifically, it is the probability of scoring 4 goals, given that the goal-scoring rate is exactly 4.0.

So, some likelihoods are probability masses — but not all.

Density¶

Now suppose, again, that we know the goal scoring rate is exactly 3, but now we want to know how long it will be until the next goal. If we model goal scoring as a Poisson process, the time until the next goal follows an exponential distribution with a rate parameter, lam=3.

Because the exponential distribution is continuous, it has a probability density function (PDF) rather than a probability mass function (PMF). We can approximate the distribution by evaluating the exponential PDF at a set of equally-spaced times, ts.

SciPy’s implementation of the exponential distribution does not take lam as a parameter, so we have to set scale=1/lam.

The PDF is a function of t with lam as a fixed parameter. Here’s what it looks like.

Notice that the values on the y-axis extend above 1. That would not be possible if they were probability masses, but it is possible because they are probability densities.

By themselves, probability densities are hard to interpret. As an example, we can pick an arbitrary element from ts and the corresponding element from ps.

So the probability density at t=0.5 is about 0.67. What does that mean? Not much.

To get something meaningful, we have to compute an area under the PDF. For example, if we want to know the probability that the first goal is scored during the first half of a game, we can compute the area under the curve from t=0 to t=0.5.

We can use a slice index to select the elements of ps and ts in this interval, and NumPy’s trapz function, which uses the trapezoid method to compute the area under the curve.

The probability of a goal in the first half of the game is about 78%. To check that we got the right answer, we can compute the same probability using the exponential CDF.

Considering that we used a discrete approximation of the PDF, our estimate is pretty close.

This example provides an operational definition of a probability density: it’s something you can add up over an interval — or integrate — to get a probability mass.

Likelihood and Density¶

Now let’s suppose that we don’t know the parameter lam and we want to use data to estimate it. And suppose we observe a game where the first goal is scored at t=0.5. As we did when we estimated the parameter mu of the Poisson distribution, we can find the value of lam that maximizes the likelihood of this data.

First we’ll define a range of possible values of lam.

Then for each value of lam, we can evaluate the exponential PDF at the observed time t=0.5 — using errstate to ignore the “division by zero” warning when lam is 0.

The result is a likelihood function, which is a function of lam with a fixed values of t. Here’s what it looks like.

Again, we can use argmax to find the index where the value of ls is maximized, and look up the corresponding value of lams.

If the first goal is scored at t=0.5, the value of lam that maximizes the likelihood of this observation is 2.

Now let’s look more closely at those likelihoods. If we select the corresponding element of ls, the result is a probability density.

Specifically, it’s the value of the exponential PDF with parameter 2, evaluated at t=0.5.

So, some likelihoods are probability densities — but as we’ve already seen, not all.

Discussion¶

What have we learned?

• In the first example, we evaluated a Poisson PMF at discrete values of k with a fixed parameter, mu. The results were probability masses.

• In the second example, we evaluated the same PMF for possible values of a parameter, mu, with a fixed value of k. The result was a likelihood function where each point is a probability mass.

• In the third example, we evaluated an exponential PDF at possible values of t with a fixed parameter, lam. The results were probability densities, which we integrated over an interval to get a probability mass.

• In the fourth example, we evaluated the same PDF at possible values of a parameter, lam, with a fixed value of t. The result was a likelihood function where each point is a probability density.

A PDF is a function of an outcome — like the number of goals scored or the time under the first goal — given a fixed parameter. If you evaluate a PDF, you get a probability density. If you integrate density over an interval, you get a probability mass.

A likelihood function is a function of a parameter, given a fixed outcome. If you evaluate a likelihood function, you might get a probability mass or a density, depending on whether the outcome is discrete or continuous. Either way, evaluating a likelihood function at a single point doesn’t mean much by itself. A common use of a likelihood function is finding a maximum likelihood estimator.

As OP says, “Probability density and likelihood are not the same thing”, but the distinction is not clear because they are not completely distinct things, either.

• A probability density can be a likelihood, but not all densities are likelihoods.

• A likelihood can be a probability density, but not all likelihoods are densities.

I hope that helps!

Data Q&A: Answering the real questions with Python

Copyright 2024 Allen B. Downey

License: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International

PMFs and PDFs¶

Here’s a question from the Reddit statistics forum.

I met a basic problem in pdf and pmf. I perform a grid approximation on bayesian problem. After normalizing the vector, I got a discretized pmf. Then I want to draw pmf and pdf on a plot to check if they are similar distribution. However, the pmf doesn’t resemble the pdf at all. The instruction told me that I need to sample from my pmf then draw a histogram with density for comparison. It really works, but why can’t I directly compare them?

In Think Bayes I used this kind of discrete approximation in almost every chapter, so this issue came up a lot! There are at least two good solutions:

• Normalize the PDF and PMF so they are on the same scale, or

• Use CDFs.

I’ll demonstrate both.

Baseball¶

As an example, I’ll solve an exercise from Chapter 4 of Think Bayes:

In Major League Baseball, most players have a batting average between .230 and .300, which means that their probability of getting a hit is between 0.23 and 0.30.

Suppose a player appearing in their first game gets 3 hits out of 3 attempts. What is the posterior distribution for their probability of getting a hit?

To represent the prior distribution, I’ll use a beta distribution with parameters I chose to be consistent with the expected range of batting averages.

Here’s what the PDF of this distribution looks like.

Unlike probability masses, probability densities can exceed 1. But the area under the curve should be 1, which we can check using trapz, which is a NumPy function that computes numerical integrals using the trapezoid rule.

Within floating-point error, the area under the PDF is 1. To do the Bayesian update, I’ll put these values in a Pmf object and normalize it so the sum of the probability masses is 1.

Now we can use binom to compute the probability of the data for each possible batting average in qs.

To compute the posterior distribution, we multiply the prior by the likelihood and normalize again so the sum of the posterior Pmf is 1.

The result is a discrete approximation of the actual posterior distribution — so let’s see how close it is.

Because the beta distribution is the conjugate prior of the binomial likelihood function, the posterior is also a beta distribution, with parameters updated to reflect the data: 3 successes and 0 failures.

Here’s what this theoretical posterior distribution looks like compared to our numerical approximation.

Oops! Something has gone wrong. I assume this is what OP meant by “the pmf doesn’t resemble the pdf at all”.

The problem is that the PMF is normalized so the total of the probability masses is 1, and the PDF is normalized so the area under the curve is 1. They are not on the same scale, so the y-axis in this figure is different for the two curves.

To fix the problem, we can find the area under the PMF.

And divide through to create a discrete approximation of the posterior PDF.

Now we can compare density to density.

The curves are visually indistinguishable, and the numerical differences are small.

As an aside, note that the posterior and prior distributions are not very different. The prior mean is 0.267 and the posterior mean is 0.281. If a rookie goes 3 for 3 in their first game, that’s a good start, but it doesn’t mean they are the next Ted Williams.

As an alternative to comparing PDFs, we could convert the PMF to a CDF, which contains the cumulative sum of the probability masses.

And compare to the mathematical CDF of the beta distribution.

In this example, I plotted the discrete approximation of the CDF as a step function — which is technically what it is — to highlight how it overlaps with the beta distribution.

Discussion¶

Probability density is hard to define — the best I can do is usually, “It’s something that you can integrate to get a probability mass”. And when you work with probability densities computationally, you often have to discretize them, which can add another layer of confusion.

One way to distinguish PMFs and PDFs is to remember that PMFs are normalized so sum of the probability masses is 1, and PDFs are normalized so the area under the curve is 1. In general, you can’t plot PMFs and PDFs on the same axes because they are not in the same units.

Data Q&A: Answering the real questions with Python

Copyright 2024 Allen B. Downey

License: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International

Standardization and Normalization¶

Here’s a question from the Reddit statistics forum.

I want to write a research article that has regression analysis in it. I normalized my independent variables and want to include in the article the results of a statistical test showing that all variables are normal. I normalized using the scale function in R and some custom normalization functions I found online but whatever I do the new data fails the Shapiro Wilkinson and KS test on some columns? What to do?

There might be a few points of confusion here:

• One is the idea that the independent variables in a regression model have to follow a normal distribution. This is a common misconception. Ordinary least squares regression assumes that the residuals follow a normal distribution — the dependent and independent variables don’t have to.

• Another is the idea that statistical tests are useful for checking whether a variable follows a normal distribution. As I’ve explained in other articles, these tests don’t do anything useful.

• The question might also reveal confusion about what “normalization” means. In the context of regression models, it usually means scaling a variable so its range is between 0 and 1. Its sounds like OP might be using it to mean transforming a variable so it follows a normal distribution.

In general, transforming an independent variable to normal is not a good idea. It has no benefit, and it changes the estimated parameters for no justified reason. Let me explain.

Happiness¶

As an example, I’ll use data from the World Happiness Report, which uses survey data from 153 countries to explore the relationship between self-reported happiness and six potentially predictive factors:

• Income as represented by per capita GDP.

• Social support

• Healthy life expectancy at birth

• Freedom to make life choices

• Generosity

• Perceptions of corruption

The dependent variable, happiness, is the national average of responses to the “Cantril ladder question” used by the Gallup World Poll:

Please imagine a ladder with steps numbered from zero at the bottom to 10 at the top. The top of the ladder represents the best possible life for you and the bottom of the ladder represents the worst possible life for you. On which step of the ladder would you say you personally feel you stand at this time?

The data they used is available here.

We can read the data into a Pandas DataFrame.

I’ll select the columns we’re interested in and give them shorter names.

Notice that GDP is already on a log scale, which is generally a good idea. The other variables are in a variety of units and different scales.

Now, contrary to the advice OP was given, let’s run a regression model without even looking at the data.

Because the independent variables are on different scales, the estimated parameters are in different units. For example, life_exp is healthy life expectancy at birth in units of years, so the estimated parameter, 0.035, indicates that a difference of one year of life expectancy between countries is associated with an increase of 0.035 units on the Cantril ladder.

Now let’s check retroactively whether this dataset is consistent with the assumption that the residuals follow a normal distribution. I’ll use the following functions to compare the CDF of the residuals to a normal model with the same mean and standard deviation.

The normal model fits the residuals well enough that the deviations are not a concern. This regression model is just fine with no transformations required.

But suppose we follow the advice OP received and check whether the dependent and independent variables follow normal distributions.

Looking for trouble¶

Here are the distributions of the variables compared to a normal model. Sometimes the model fits pretty well, sometimes not.

If we ran a statistical test, most of these would fail. But we don’t care — regression models don’t require these variables to follow normal distributions. And when we make this kind of comparison across countries, there no reason to expect them to.

Standardize¶

Nevertheless, there are reasons we might want to transform the independent variables before running a regression model — one is to quantify the “importance” of the different factors. We can do that by standardizing the variables, which means transforming them to have mean 0 and standard deviation 1.

In the untransformed variables, the means vary in magnitude from about 0.1 to 64.

And the standard deviations vary from about 0.1 to 7.

And, as I’ve already noted, they are expressed in different units. There is no meaningful way to compare the parameter of life_exp, which is steps of the Cantril ladder per year of life expectancy, with the parameter of corruption, which is in steps of the ladder per percentage point. But we can make these comparisons meaningful by standardizing the variables — that is, subtracting off the mean and dividing by the standard deviation.

After transformation, the means are all close to 0.

And the standard deviations are all close to 1.

Here’s the regression with the transformed variables.

The intercept is close to 0 — that’s a consequence of how the math works out. And now the magnitudes of the parameters indicate how much a change in each independent variable, expressed as a multiple of its standard deviation, is associated with a change in the dependent variables, also as a multiple of its standard deviation.

By this metric, social is the most important factor, followed closely by log_gdp and life_exp. generosity is the least important factor, at least as its quantified by this variable.

Normalizing¶

An alternative to standardization is normalization, which transforms a variable so its range is between 0 and 1. To be honest, I’m not sure what the point of normalization is — it makes the results a little harder to interpret, and it doesn’t have any advantages I can think of.

But just for completeness, here’s how it’s done.

As intended, the normalized variables have the same range.

But as a result they have somewhat different means and standard deviations.

Here’s the regression with normalized variables.

We’ll look more closely at those results soon, but first let’s look at one more preprocessing option, transforming values to follow a normal distribution.

Transform to normal¶

Here’s how we transform values to a normal distribution.

The ps are the cumulative probabilities; the zs are the corresponding quantiles in a standard normal distribution (ppf computes the “percent point function” which is an unnecessary name for the inverse CDF). Inside the loop, we sort transformed by one of the columns and then assign the zs in that order.

The transformed means are all close to 0.

And the standard deviations are close to 1 (but not exact because the tails of the distribution are cut off).

As intended, the transformed variables follow a normal distribution.

Here’s the regression model with the transformed values.

Now let’s compare the estimated parameters with the three transformations.

The results with standardized variables are the easiest to interpret, so in that sense they are “right”. The other transformations have no advantages over standardization, and they produce somewhat different parameters.

Discussion¶

Regression does not require the dependent or independent variables to follow a normal distribution. It only assumes that the distribution of residuals is approximately normal, and even that requirement is not strict — regression is quite robust.

You do not need to check whether any of these variables follows a normal distribution, and you definitely should not use a statistical test.

As part of your usual exploratory data analysis, you should look at the distribution of all variables, but that’s primarily to detect any anomalies, outliers, or really extreme distributions — not to check whether they fit normal distributions.

If you want to use the parameters of the model to quantify the importance of the independent variables, use standardization. There’s no reason to use normalization, and definitely no reason to transform to a normal distribution.

Data Q&A: Answering the real questions with Python

Copyright 2024 Allen B. Downey

License: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International