python – Probably Overthinking It

Think DSP v1.1

June 3, 2020 AllenDowney

For the last week or so I have been working on an update to Think DSP. The latest version is available now from Green Tea Press. Here are some of the changes I made:

Running on Colab

All notebooks now run on Colab. Judging by my inbox, many readers find it challenging to download and run the code. Running on Colab is a lot easier.

If you want to try an example, here’s a preview of Chapter 1. And if you want to see where we’re headed, here’s a preview of Chapter 10. You can get to the rest of the notebooks from here.

No more thinkplot

For the first edition, I used a module called thinkplot that provides functions that make it easier to use Matplotlib. It also overrides some of the default options.

But since I wrote the first edition, Matplotlib has improved substantially. I found I was able to eliminate thinkplot with minimal changes. As a result, the code is simpler and the figures look better.

Still using thinkdsp

I provide a module called thinkdsp that contains classes and functions used throughout the book. I think this module is good for learners. It lets me hide details that would otherwise be distracting. It lets me present some topics “top-down”, meaning that we learn how to use some features before we know how they work.

And when you learn the API provided by thinkdsp, you are also learning about DSP. For example, thinkdsp provides classes called Signal, Wave, and Spectrum.

A Signal represents a continuous function; a Wave represents a sequence of discrete samples. So Signal provides make_wave, but Wave does not provide make_signal. When you use this API, you understand implicitly that this is a one-way operation: you can sample a Signal to get a Wave, but you cannot recover a Signal from a Wave.

On the other hand, you can convert from Wave to Spectrum and from Spectrum to Wave, which implies (correctly) that they are equivalent representations of the same information. Given one, you can compute the other.

I realize that not everyone loves it when a book uses a custom library like thinkdsp. When people don’t like Think DSP, this is the most common reason. But looking at thinkdsp with fresh eyes, I am doubling down; I still think it’s a good way to learn.

Less object-oriented

Nevertheless, I found a few opportunities to simplify the code, and in particular to make it less object-oriented. I generally like OOP, but I acknowledge that there are drawbacks. One of the biggest is that it can be hard to keep an inheritance hierarchy in your head and easy to lose track of what classes provide which methods.

I still think the template pattern is a good way to present a framework: the parent class provides the framework and child classes fill in the details.

However, based on feedback from readers, I have come to realize that object-oriented programming is not as universally known and loved as I assumed.

In several places I found that I could eliminate object-oriented features and simplify the code without losing explanatory power.

Pretty, pretty good

Coming back to this book after some time, I think it’s pretty good. If you are interested in digital signal processing, I think the computation-first approach is a good way to get started. And if you are not interested in digital signal processing, maybe I can change your mind!

Here are the links again:

Here’s the latest version from Green Tea Press.
Here’s a preview of Chapter 1. that you can run in a browser.
And here’s a preview of Chapter 10.
You can get to the rest of the notebooks from here.

The Dartboard Paradox

October 18, 2019 AllenDowney

On November 5, 2019, I will be at PyData NYC to give a talk called The Inspection Paradox is Everywhere. Here’s the abstract:

The inspection paradox is a statistical illusion you’ve probably never heard of. It’s a common source of confusion, an occasional cause of error, and an opportunity for clever experimental design. And once you know about it, you see it everywhere.

The examples in the talk include social networks, transportation, education, incarceration, and more. And now I am happy to report that I’ve stumbled on yet another example, courtesy of John D. Cook.

In a blog post from 2011, John wrote about the following counter-intuitive truth:

For a multivariate normal distribution in high dimensions, nearly all the probability mass is concentrated in a thin shell some distance away from the origin.

John does a nice job of explaining this result, so you should read his article, too. But I’ll try to explain it another way, using a dartboard.

If you are not familiar with the layout of a “clock” dartboard, it looks like this:

I got the measurements of the board from the British Darts Organization rules, and drew the following figure with dimensions in mm:

Now, suppose I throw 100 darts at the board, aiming for the center each time, and plot the location of each dart. It might look like this:

Suppose we analyze the results and conclude that my errors in the x and y directions are independent and distributed normally with mean 0 and standard deviation 50 mm.

Assuming that model is correct, then, which do you think is more likely on my next throw, hitting the 25 ring (the innermost red circle), or the triple ring (the middlest red circle)?

It might be tempting to say that the 25 ring is more likely, because the probability density is highest at the center of the board and lower at the triple ring.

We can see that by generating a large sample, generating a 2-D kernel density estimate (KDE), and plotting the result as a contour.

In the contour plot, darker color indicates higher probability density. So it sure looks like the inner ring is more likely than the outer rings.

But that’s not right, because we have not taken into account the area of the rings. The total probability mass in each ring is the product of density and area (or more precisely, the density integrated over the area).

The 25 ring is more dense, but smaller; the triple ring is less dense, but bigger. So which one wins?

In this example, I cooked the numbers so the triple ring wins: the chance of hitting triple ring is about 6%; the chance of hitting the double ring is about 4%.

If I were a better dart player, my standard deviation would be smaller and the 25 ring would be more likely. And if I were even worse, the double ring (the outermost red ring) might be the most likely.

Inspection Paradox?

It might not be obvious that this is an example of the inspection paradox, but you can think of it that way. The defining characteristic of the inspection paradox is length-biased sampling, which means that each member of a population is sampled in proportion to its size, duration, or similar quantity.

In the dartboard example, as we move away from the center, the area of each ring increases in proportion to its radius (at least approximately). So the probability mass of a ring at radius r is proportional to the density at r, weighted by r.

We can see the effect of this weighting in the following figure:

The blue line shows estimated density as a function of r, based on a sample of throws. As expected, it is highest at the center, and drops away like one half of a bell curve.

The orange line shows the estimated density of the same sample weighted by r, which is proportional to the probability of hitting a ring at radius r.

It peaks at about 60 mm. And the total density in the triple ring, which is near 100 mm, is a little higher than in the 25 ring, near 10 mm.

If I get a chance, I will add the dartboard problem to my talk as yet another example of length-biased sampling, also known as the inspection paradox.

You can see my code for this example in this Jupyter notebook.

UPDATE November 6, 2019: This “thin shell” effect has practical consequences. This excerpt from The End of Average talks about designing the cockpit of a plan for the “average” pilot, and discovering that there are no pilots near the average in 10 dimensions.

Left, right, part 4

August 6, 2019 AllenDowney

In the first article in this series, I looked at data from the General Social Survey (GSS) to see how political alignment in the U.S. has changed, on the axis from conservative to liberal, over the last 50 years.

In the second article, I suggested that self-reported political alignment could be misleading.

In the third article I looked at responses to this question:

Do you think most people would try to take advantage of you if they got a chance, or would they try to be fair?

And generated seven “headlines” to describe the results.

In this article, we’ll use resampling to see how much the results depend on random sampling. And we’ll see which headlines hold up and which might be overinterpretation of noise.

Overall trends

In the previous article we looked at this figure, which was generated by resampling the GSS data and computing a smooth curve through the annual averages.

This image has an empty alt attribute; its file name is image.png

If we run the resampling process two more times, we get somewhat different results:

Now, let’s review the headlines from the previous article. Looking at different versions of the figure, which conclusions do you think are reliable?

Absolute value: “Most respondents think people try to be fair.”
Rate of change: “Belief in fairness is falling.”
Change in rate: “Belief in fairness is falling, but might be leveling off.”

In my opinion, the three figures are qualitatively similar. The shapes of the curves are somewhat different, but the headlines we wrote could apply to any of them.

Even the tentative conclusion, “might be leveling off”, holds up to varying degrees in all three.

Grouped by political alignment

When we group by political alignment, we have fewer samples in each group, so the results are noisier and our headlines are more tentative.

Here’s the figure from the previous article:

This image has an empty alt attribute; its file name is image-1.png

And here are two more figures generated by random resampling:

Now we see more qualitative differences between the figures. Let’s review the headlines again:

Absolute value: “Moderates have the bleakest outlook; Conservatives and Liberals are more optimistic.” This seems to be true in all three figures, although the size of the gap varies substantially.

Rate of change: “Belief in fairness is declining in all groups, but Conservatives are declining fastest.” This headline is more questionable. In one version of the figure, belief is increasing among Liberals. And it’s not at all clear the the decline is fastest among Conservatives.

Change in rate: “The Liberal outlook was declining, but it leveled off in 1990.” The Liberal outlook might have leveled off, or even turned around, but we could not say with any confidence that 1990 was a turning point.

Change in rate: “Liberals, who had the bleakest outlook in the 1980s, are now the most optimistic”. It’s not clear whether Liberals have the most optimistic outlook in the most recent data.

As we should expect, conclusions based on smaller sample sizes are less reliable.

Also, conclusions about absolute values are more reliable than conclusions about rates, which are more reliable than conclusions about changes in rates.

Left, right, part 3

August 1, 2019 AllenDowney

In the second article, I suggested that self-reported political alignment could be misleading.

In this article we’ll look at results from questions related to “outlook”, that is, how the respondents see the world and people in it.

Specifically, the questions are:

fair: Do you think most people would try to take advantage of you if they got a chance, or would they try to be fair?
trust: Generally speaking, would you say that most people can be trusted or that you can’t be too careful in dealing with people?
helpful: Would you say that most of the time people try to be helpful, or that they are mostly just looking out for themselves?

Do people try to be fair?

Let’s start with fair. The responses are coded like this:

1    Take advantage
2    Fair
3    Depends

To put them on a numerical scale, I recoded them like this:

1    Fair
0.5  Depends
0    Take advantage

I flipped the axis so the more positive answer is higher, and put “Depends” in the middle. Now we can plot the mean response by year, like this:

Looking at a figure like this, there are three levels we might describe:

Absolute value: “Most respondents think people try to be fair.”
Rate of change: “Belief in fairness is falling.”
Change in rate: “Belief in fairness is falling, but might be leveling off.”

For any of these qualitative descriptions, we could add quantitative estimates. For example, “About 55% of U.S. residents think people try to be fair”, or “Belief in fairness has dropped 10 percentage points since 1970”.

Statistically, the estimates of absolute value are probably reliable, but we should be more cautious estimating rates of change, and substantially more cautious talking about changes in rates. We’ll come back to this issue, but first let’s look at breakdowns by group.

Outlook and political alignment

In the previous article I grouped respondents by self-reported political alignment: Conservative, Moderate, or Liberal.

We can use these groups to see the relationship between outlook and political alignment. For example, the following figure shows the average response to the fairness question, grouped by political alignment and plotted over time:

Results like these invite comparisons between groups, and we can make those comparisons at several levels. Here are some potential headlines for this figure:

Absolute value: “Moderates have the bleakest outlook; Conservatives and Liberals are more optimistic.”
Rate of change: “Belief in fairness is declining in all groups, but Conservatives are declining fastest.”
Change in rate: “The Liberal outlook was declining, but it leveled off in 1990.” or “Liberals, who had the bleakest outlook in the 1980s, are now the most optimistic”.

Because we divided the respondents into three groups, the sample size in each group is smaller. Statistically, we need to be more skeptical about our estimates of absolute level, even more skeptical about rates of change, and extremely skeptical about changes in rates.

In the next article, I’ll use resampling to quantify the uncertainly of these estimates, and we’ll see how many of these headlines hold up.

Left, right, part 2

July 27, 2019 AllenDowney

In the previous article, I looked at data from the General Social Survey (GSS) to see how political alignment in the U.S. has changed, on the axis from conservative to liberal, over the last 50 years.

The GSS asks respondents where they place themselves on a 7-point scale from “extremely liberal” (1) to “extremely conservative” (7), with “moderate” in the middle (4).

In the previous article I computed the mean and standard deviation of the responses as a way of quantifying the center and spread of the distribution. But it can be misleading to treat categorical responses as if they were numerical. So let’s see what we can do with the categories.

The following plot shows the fraction of respondents who place themselves in each category, plotted over time:

My initial reaction is that these lines are mostly flat. If political alignment is changing in the U.S., it is changing slowly, and the changes might not matter much in practice.

If we look more closely, it seems like the number of people who consider themselves “extreme” is increasing, and the number of moderates might be decreasing. The following plot shows a closer look at the extremes.

There is some evidence of polarization here, but we should not make too much of it. People who consider themselves extreme are still less than 10% of the population, and moderates are still the biggest group, at almost 40%.

To get a better sense of what’s happening with the other groups, I reduced the number of categories to 3: “Conservative” at any level, “Liberal” at any level, and “Moderate”. Here’s what the plot looks like with these categories:

Moderates make up a plurality; conservatives are the next biggest group, followed by liberals.

From 1974 to 1990, the number of people who call themselves “Conservative” was increasing, but it has decreased ever since. And the number of “Liberals” has been increasing since 2000.

At least, that’s what this plot seems to show. We should be careful about over-interpreting patterns that might be random noise. And we might not want to take these categories too seriously, either.

The hazards of self-reporting

There are several problems with self-reported labels like this.

First, political beliefs are multi-dimensional. “Conservative” and “liberal” are labels for collections of ideas that sometimes go together. But most people hold a mixture of these beliefs.

Also, these labels are relative; that is, when someone says they are conservative, what they often mean is that they are more conservative than the center of the population, or where they think the center is, for the population they have in mind.

Finally, nearly all survey responses are subject to social desirability bias, which is the tendency of people to give answers that make them look better or feel better about themselves.

Over time, the changes we see in these responses depend on actual changes in political beliefs, but they also depend on where the center of the population is, where people think the center is, and the perceived desirability of the labels “liberal”, “conservative”, and “moderate”.

So, in the next article we’ll look more closely at changes in beliefs and attitudes, not just labels.

I am planning to turn these articles into a case study for an upcoming Data Science class, so I welcome comments and questions.

The code I used to generate these figures is in this Jupyter notebook.

Right, left, apart, together?

July 26, 2019 AllenDowney

Is the United States getting more conservative? With the rise of the alt-right, Republican control of Congress, and the election of Donald Trump, it might seem so.

Or is the country getting more liberal? With the 2015 Supreme Court decision supporting same-sex marriage, the incremental legalization of marijuana, and recent proposals to expand public health care, you might think so.

Or maybe the country is becoming more polarized, with moderates choosing sides and partisans moving to the extremes.

In a series of articles, I’ll use data from the General Social Survey (GSS) to explore these questions. The GSS goes back to 1972; every second year they survey a representative sample of U.S. residents and ask questions about their political beliefs. Many of the questions have been unchanged for almost 50 years, making it possible to observe long-term trends.

In this article, I’ll look at political alignment, that is, whether the respondents consider themselves liberal or conservative. In subsequent articles, I’ll explore their political beliefs on a range of topics.

Political alignment

From 1974 to the most recent cycle in 2018, the GSS asked the following question, “We hear a lot of talk these days about liberals and conservatives.
I’m going to show you a seven-point scale on which the political views that people might hold are arranged from extremely liberal–point 1–to extremely conservative–point 7. Where would you place yourself on this scale?”

The following figure shows the distribution of responses in 1974 and 2018.

In 2018, it looks like there are more 1s (Extremely Liberal) and maybe more 7s (Extremely Conservative). So this figure provides some evidence of polarization.

We can get a better sense of the long term trend by taking the mean of the 7-point scale and plotting it over time. By treating this scale as a numerical quantity, I’m making assumptions about the spacing between the values. The numbers we get don’t mean much in absolute terms, but they provide a quick look at the trend.

It looks like the “center of mass” was increasing until about 1990, which means more conservative on this scale, and has been decreasing ever since. On average the country might be a little more conservative now than it was in 1974.

With the same caveat about treating this scale as a numerical quantity, we can also compute the standard deviation, which measures average distance from the mean, as a way of quantifying polarization.

The trend is clearly increasing, indicating increasing polarization, but with the way we computed these numbers, it’s hard to get a sense of how substantial the increase is in practical terms.

In the next article, I’ll look more closely at changes in political alignment over time.

I am planning to turn these articles into a case study for an upcoming Data Science class, so I welcome comments and questions.

The code I used to generate these figures is in this Jupyter notebook.

Matplotlib animation in Jupyter

July 25, 2019 AllenDowney

For two of my books, Think Complexity and Modeling and Simulation in Python, many of the examples involve animation. Fortunately, there are several ways to do animation with Matplotlib in Jupyter. Unfortunately, none of them is ideal.

FuncAnimation

Until recently, I was using FuncAnimation, provided by the matplotlib.animation package, as in this example from Think Complexity. The documentation of this function is pretty sparse, but if you want to use it, you can find examples.

For me, there are a few drawbacks:

It requires a back end like ffmpeg to display the animation. Based on my email, many readers have trouble installing packages like this, so I avoid using them.
It runs the entire computation before showing the result, so it takes longer to debug, and makes for a less engaging interactive experience.
For each element you want to animate, you have to use one API to create the element and another to update it.

For example, if you are using imshow to visualize an array, you would run

    im = plt.imshow(a, **options)

to create an AxesImage, and then

    im.set_array(a)

to update it. For beginners, this is a lot to ask. And even for experienced people, it can be hard to find documentation that shows how to update various display elements.

As another example, suppose you have a 2-D array and plot it like this:

    plot(a)

The result is a list of Line2D objects. To update them, you have to traverse the list and invoke set_xdata() on each one.

Updating a display is often more complicated than creating it, and requires substantial navigation of the documentation. Wouldn’t it be nice to just call plot(a) again?

Clear output

Recently I discovered simpler alternative using clear_output() from Ipython.display and sleep() from the time module. If you have Python and Jupyter, you already have these modules, so there’s nothing to install.

Here’s a minimal example using imshow:

%matplotlib inline

import numpy as np
from matplotlib import pyplot as plt
from IPython.display import clear_output
from time import sleep

n = 10
a = np.zeros((n, n))
plt.figure()

for i in range(n):
    plt.imshow(a)
    plt.show()
    a[i, i] = 1
    sleep(0.1)
    clear_output(wait=True)

The drawback of this method is that it is relatively slow, but for the examples I’ve worked on, the performance has been good enough.

In the ModSimPy library, I provide a function that encapsulates this pattern:

def animate(results, draw_func, interval=None):
    plt.figure()
    try:
        for t, state in results.iterrows():
            draw_func(state, t)
            plt.show()
            if interval:
                sleep(interval)
            clear_output(wait=True)
        draw_func(state, t)
        plt.show()
    except KeyboardInterrupt:
        pass

results is a Pandas DataFrame that contains results from a simulation; each row represents the state of a system at a point in time.

draw_func is a function that takes a state and draws it in whatever way is appropriate for the context.

interval is the time between frames in seconds (not counting the time to draw the frame).

Because the loop is wrapped in a try statement that captures KeyboardInterrupt, you can interrupt an animation cleanly.

You can see an example that uses this function in this notebook from Chapter 22 of Modeling and Simulation in Python, and you can run it on Binder.

And here’s an example from Chapter 6 of Think Complexity, which you can also run on Binder.

Local regression in Python

April 1, 2019 AllenDowney

I love data visualization make-overs (like this one I wrote a few months ago), but sometimes the tone can be too negative (like this one I wrote a few months ago).

Sarah Leo, a data journalist at The Economist, has found the perfect solution: re-making your own visualizations. Here’s her tweet.

And here’s the link to the article, which you should go read before you come back here.

One of her examples is the noisy line plot on the left, which shows polling results over time.

Here’s Leo’s explanation of what’s wrong and why:

Instead of plotting the individual polls with a smoothed curve to show the trend, we connected the actual values of each individual poll. This happened, primarily, because our in-house charting tool does not plot smoothed lines. Until fairly recently, we were less comfortable with statistical software (like R) that allows more sophisticated visualisations. Today, all of us are able to plot a polling chart like the redesigned one above.

This confession made me realize that I am in the same boat they were in: I know about local regression, but I don’t use it because I haven’t bothered to learn the tools.

Fortunately, filling this gap in my toolkit took less than an hour. The StatsModels library provides lowess, which computes locally weighted scatterplot smoothing.

I grabbed the data from The Economist and read it into a Pandas DataFrame. Then I wrote the following function, which takes a Pandas Series, computes a LOWESS, and returns a Pandas Series with the results:

from statsmodels.nonparametric.smoothers_lowess import lowess

def make_lowess(series):
    endog = series.values
    exog = series.index.values

    smooth = lowess(endog, exog)
    index, data = np.transpose(smooth)

    return pd.Series(data, index=pd.to_datetime(index))

And here’s what the results look like:

The smoothed lines I got look a little different from the ones in The Economist article. In general the results depends on the parameters we give LOWESS. You can see all the details in this Jupyter notebook.

Thanks to Sarah Leo for inspiring me to learn to use LOWESS, and for providing the data I used to replicate the results.

Probably Overthinking It

Data science, Bayesian Statistics, and other ideas

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