Matplotlib animation in Jupyter

Matplotlib animation in Jupyter

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.

Report from SciPy 2019

Report from SciPy 2019

Greetings from Austin and SciPy 2019. In this post, I’ve collected the materials for my tutorials and talks.

On Monday morning I presented Bayesian Statistics Made Simple in an extended 4-hour format:

In the afternoon I presented a tutorial on Complexity Science:

On Tuesday I presented a short talk for the teen track. Here are the slides, with links to the two notebooks on Binder:

And tomorrow I’m presenting a talk, “Generational Changes in Support for Gun Laws: A Case Study in Computational Statistics”:

Abstract: In the United States, support for gun control has been declining among all age groups since 1990; among young adults, support is substantially lower than among previous generations. Using data from the General Social Survey (GSS), I perform age-period-cohort analysis to measure generational effects.
In this talk, I demonstrate a computational approach to statistics that replaces mathematical analysis with random simulation. Using Python and libraries like NumPy and StatsModels, we can define basic operations — like resampling, filling missing values, modeling, and prediction — and assemble them into a data analysis pipeline.

If you are at SciPy, my talk is Thursday morning from 10:20 to 10:50 in the Zlotnik Ballroom.

Backsliding on the path to godlessness

Backsliding on the path to godlessness

In the last 30 years, college students have become much less religious. The fraction who say they have no religious affiliation tripled, from about 10% to 30%. And the fraction who say they have attended a religious service in the last year fell from 85% to 70%.

I’ve been following this trend for a while, using data from the CIRP Freshman Survey. The most recently published data is from “120,357 first-time, full-time students who entered 168 U.S. colleges and universities in the fall of 2017.”

One of the questions asks students to select their “current religious preference,” from a choice of seventeen common religions, “Other religion,” “Atheist”, “Agnostic”, or “None.”  

The options “Atheist” and “Agnostic” were added in 2015.  For consistency with previous years, I compare the “Nones” from previous years with the sum of “None”, “Atheist” and “Agnostic” since 2015.

The following figure shows the fraction of Nones over the 50 years of the survey.

Percentage of students with no religious preference from 1968 to 2017.

The blue line shows actual data through 2017; the gray line shows a quadratic fit.  The light gray region shows a 90% predictive interval.

For the first time since 2011, the fraction of Nones decreased this year, reverting to the trend line.

Another question asks students how often they “attended a religious service” in the last year. The choices are “Frequently,” “Occasionally,” and “Not at all.” Students are instructed to select “Occasionally” if they attended one or more times.

Here is the fraction of students who reported any religious attendance in the last year:

Percentage of students who reported attending a religious service in the previous year.

Slightly more students reported attending a religious service in 2017 than in the previous year, contrary to the long-term trend.

Female students are more religious than male students. The following graph shows the gender gap over time, that is, the difference in percentages of male and female students with no religious affiliation.

Difference in religious affiliation between male and female students.

The gender gap was growing until recently. It has shrunk in the last 3-4 years, but since it varies substantially from year to year, it is hard to rule out random variation.

Data from 2018 should be available soon; I’ll post an update when I can.

Data Source

The American Freshman: National Norms Fall 2017
Stolzenberg, E. B., Eagan, M. K., Aragon, M. C., Cesar-Davis, N. M., Jacobo, S., Couch, V., & Rios-Aguilar, C.
Higher Education Research Institute, UCLA.
Apr 2019

This and all previous reports are available from the HERI publications page.

Foundations of data science?

Foundations of data science?

“Foundation” is one of several words I would like to ban from all discussion of higher education.  Others include “liberal arts”, “rigor”, and “service class”, but I’ll write about them another time.  Right now, “foundation” is on my mind because of a new book from Microsoft Research, Foundations of Data Science, by Avrim Blum, John Hopcroft, and Ravindran Kannan.

The goal of their book is to “cover the theory we expect to be useful in the next 40 years, just as an understanding of automata theory, algorithms, and related topics gave students an advantage in the last 40 years.”

As an aside, I am puzzled by their use of “advantage” here: who did those hypothetical students have an advantage over?  I don’t think competitive advantage is the primary goal of learning. If a theory is useful, it helps you solve problems and make the world a better place, not just crush your enemies.

I am also puzzled by their use of “foundation”, because it can mean two contradictory things:

  1. The most useful ideas in a field; the things you should learn first.
  2. The most theoretical ideas in a field; the things you should use to write mathematical proofs.

Both kinds of foundation are valuable.  If you identify the right things to learn first, you can give students powerful tools quickly, they can work on real problems and have impact, and they are more likely to be excited about learning more.  And if you find the right abstractions, you can build intuition, develop insight, make connections, and create new tools and ideas.

The problems come when we confuse these meanings, assume that the most abstract ideas are the most useful, and require students to learn them first.  In higher education, confusion about “foundations” is the root of a lot of bad curriculum design.

For example, in the traditional undergraduate engineering curriculum, students take 1-2 years of math and science classes before they learn anything about engineering.  These prerequisites are called the “Math and Science Death March” because so many students don’t get through them; in the U.S., about 40% of students who start an engineering program don’t finish it, largely because of the incorrect assumption that they need two years of theory before they can start engineering.

The introduction to Foundations of Data Science hints at the first meaning of “foundation”.  The authors note that “increasingly researchers of the future will be involved with using computers to understand and extract usable information from massive data arising in applications,” which suggests that this book will help them do those things.

But the rest of the introduction makes it clear that the second meaning is what they have in mind.  

  • “Chapters 2 and 3 lay the foundations of geometry and linear algebra respectively.”
  • “We give a from-first-principles description of the mathematics and algorithms for SVD.”
  • “The underlying mathematical theory of such random walks, as well as connections to electrical networks, forms the core of Chapter 4 on Markov chains.”
  • “Chapter 9 focuses on linear-algebraic problems of making sense from data, in particular topic modeling and non-negative matrix factorization.”

The “fundamentals” in this book are abstract, mathematical, and theoretical.  The authors assert that learning them will give you an “advantage”, but if you are looking for practical tools to solve real problems, you might need to build on a different foundation.

Local regression in Python

Local regression in Python

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.

Happiness, Mental Health, Drugs, Politics, and Language

Happiness, Mental Health, Drugs, Politics, and Language

The following are abstracts from 13 projects where students in my Data Science class explore public data sets related to a variety of topics. Each abstract ends with a link to a report where you can see the details.

A Deeper Dive into US Suicides

Diego Berny and Anna Griffin

The world’s suicide rate has been decreasing over the past decade but unfortunately the United States’ rate is doing the exact opposite. Using data from the CDC and Our World in Data organizations, we explored different demographics to see if there are any patterns of vulnerable populations. We found that the group at the most risk is middle aged men. Men’s suicide rate is nearly 4 times higher than women’s and the group of adults between the ages of 45 and 59 has seen 36.5% increase over the past 17 years. When comparing their methods of suicide to their female counterparts we found that men tend to use more lethal means, resulting is less nonfatal suicide attempts. Read more

The Opioid Epidemic and Its Socioeconomic Effects

Daniel Connolly and Bryce Mann

Between 2002 and 2016, heroin use increased by 40%, while the use of other seemingly similar drugs declined in the same period. Using data from the National Survey on Drug Use and Health, we explore how the characteristics of opioid users have changed since the beginning of the epidemic. We find that so-called “late-starters” make up a new population of opioid users, as the average starting age of heroin users has increased by 2.5 years since 2002. We find a major discrepancy between the household incomes of users and nonusers as well, a discovery possibly related to socioeconomic factors like marriage. Read more

What is the Mother Tongue in U.S. Communities?

Allison Busa and Jordan Crawford-O’Banner

By watching the news, a person can assume that diversity is increasing rapidly in the United States. The current generation has been heralded as the most diverse in the history of the country. However, some Americans do not feel very positively about this change, and some even feel that the change is happening too rapidly. We decided to use the data from the U.S. Census to put these claims to the test. Using linguistic Census data, we ask “Is cultural diversity changing over time?” and “How is it spread out?” With PMFs, we analyze the number of people who speak a language other than English at home (SONELAHs). There is a wide range of SONELAHs in the U.S., from only 2 % of West Viriginians to 42% of Californians. Compared inside individual states, however, variations are less extreme. Read More

Heroin and Alcohol: Could there be a relationship?

Daphka Alius

Alcohol abuse is a disease that affects millions in the US. Similarly, opioids have become a national health crisis signaling a substantial increase in opioids use. The question under investigation is whether the same people who abuse heroin, a form of opioid, are also drinking congruously throughout the year. Using data from National Survey of Drug Use and Health, I found that people who infrequently (< 30 days/year) drink alcohol in a year are consuming heroin 1.7 times longer in a year than those who frequently (> 300 days/year) drink alcohol. Additionaly, the two variables are weakly correlated with a Pearson correlation that corresponds to -0.22. Read More

Does Health Insurance Type Lead To Opioid Addiction?

Micah Reid, Filipe Borba

The rate of opioid addiction has escalated into a crisis in recent years. Studies have linked health insurance with prescription painkiller overuse, but little has been done to investigate differences tied to health insurance type. We used data from the National Survey on Drug Use and Health from the year 2017 single out variations in drug use and abuse prevalence and duration across these groups. We found that while those with private health insurance were more likely to have used opioids than those with Medicaid/CHIP or no health insurance (57.3% compared to 45% and 47.4%, respectively), those with Medicaid/CHIP or no health insurance were more likely to have abused opioids when controlling for past opioid use (24.6% and 27.2% versus 17.6%, respectively). Those with private health insurance were also more likely to have used opioids in the past, while those with Medicaid/CHIP or no health insurance were more likely to have continued their use. This suggests that even though those with private health insurance are more likely to use opioids, those without are more likely to continue use and begin misuse once started on opiates. Read more

Finding differences between Conservatives and Liberals

Siddharth Garimella

I looked through data from the General Social Survey (GSS) to gain a better understanding about what issues conservatives and liberals differ most on. After making some guesses of my own, I separated conservative and liberal respondents, and sorted their effect sizes for every variable in the dataset segment I had available, ultimately finding three big differences between the two groups. My results suggest conservatives most notably disagree more with same-sex relationships, tend to be slightly older, and attend religious events far more often than liberals do. Read more

Exploring OxyContin Use in the United States

Ariana Olson

According to the CDC, OxyContin is among the most common prescription opioids involved in overdose death. I explored variables related to OxyContin use, both medical and non-medical, from the 2014 National Survey on Drug Use and Health (NSDUH). I found that the median age that respondents tried OxyContin for the first time in a way that wasn’t prescribed for them is around 22, and that almost all respondents who had tried OxyContin non-medically did so before the age of 50. I also found that the overwhelming majority of respondents had never used OxyContin non-medically, but out of those who had, there was an 82% probability that they had used it over 12 months prior to the survey. People who used OxyContin also reported using the drug for fewer days total per year in a way that wasn’t prescribed to them than people who used it at all, prescribed or not. Finally, I found that the median age at which people first used OxyContin in a way that wasn’t directed by a doctor increased with older age groups, and the minimum age of first trying OxyContin non-medically per age group tended to increase as the age of the groups increased. Read more

Subjective Class Compared to Income Class

Cassandra Overney

Back in my hometown, many people consider themselves middle class regardless of their incomes. I grew up confusing income class with subjective class. Now that I am living in a new environment, I am curious to see whether a discrepancy between subjective and income class exists throughout America. The main question I want to answer is: how does subjective class compare to income class?

Income is not the only factor that Americans associate with class since most respondents consider themselves to be either working or middle class. However, there are some discernable differences in subjective class based on income. For example, respondents in the lowest income class are more likely to consider themselves working class than middle class (10.7% vs 6.3%) while respondents in the highest income class are more likely to consider themselves middle class than working class (13.3% vs 4.2%). Read more

The Contribution of the Opioid Epidemic on the Falling Life Expectancy in the United States

Sabrina Pereira

In recent years, a downward trend in the Average Life Expectancy (ALE) in the US has emerged. At the same time, the number of deaths by opioid poisoning has risen dramatically. Using mortality data from the Centers for Disease Control and Prevention, I create a model to quantify the effect of the increase of opioid-related deaths on the ALE in the US. According to the model, the ALE in 2017 would have been about .46 years higher if there had been no opioid-related deaths (79.06 years, compared to the observed 78.6 years). It is only recently that these deaths have created an observable effect this large. Read more

Exploring the Opioid Epidemic

Emma Price

People who use heroin are most likely to do so between the ages of 18 and 40, whereas people who misuse opiate pain relievers are consistently likely to misuse for the first time starting in their early teens. The portion of heroin and prescribed opiate users that stay in school until they complete high school is higher than that of people who do not use opiates; however, the portion of the population of heroin users drop very quickly in their likelihood to survive through college. The rate at which people who misuse opiate pain relievers drop out of school generally follows that of non-users once the high school tipping point is past. Read more

Drug use patterns and correlations

Sreekanth Reddy Sajjala

For users of various regulated substances, their exposure to and use of them varies greatly substance to substance. The National Survey on Drug Use and Health dataset has extensive data which can allow us to view patterns and correlations in their usage. Only 40% of the people who have ever tried cocaine have used it in the past year, but almost 60% of those who have tried heroin use it atleast once a week. People who have tried cannabis tend to try alcohol at an age 15% lower than users who haven’t tried cannabis do so. Unless drug use patterns change drastically, if someone has consumed cannabis at any point in their life they are over 20 times more likely to try heroin at some point in their life. Read more

Age and Generation Affect Happiness Levels in Marriage… A Little

Ashley Swanson

Among age, time, and cohort analysis, happiness levels in marriage are most drastically affected by the age of an individual up until their early 40’s. Between age 20 and age 40, the reported percentage of happy marriages drops by -0.45% percent a year, nearly 10% over the course of those two decades. The following 4 decades see a rebound of about 8%, meaning that 90-year-olds are nearly as happy as 20-year-olds, with those in their early 40’s experiencing the lowest levels of marital happiness. However, cohort effects have the highest explanatory value with an r-value of 0.44. Those born in 1950 experience 13.3% fewer happy marriages than those born in 1900, and those born in 2000 experience an average of 10.5% more happy marriages than those born in 1950. Each of these variables has a small effect size per year, a fraction of a percentage point, but the sustained trends over the decades are significant enough to have real effects. Read more

Associations between screen time and kids’ mental health

MinhKhang Vu

Previous research on children and adolescents has suggested strong associations between screen time and their mental health, contributing to growing concerns among parents, teachers, counselors and doctors about digital technology’s negative effects on children. Using the Census Bureau’s 2017 National Survey of Children’s Health (NSCH), I investigated a large (n=21,599) national random sample of 0- to 17-year-old children in the U.S. in 2017. The NSCH collects data on the physical and emotional health of American children every year, which includes information about their screen time usage and other comprehensive well-being measures. Children who spend 3 hours or more daily using computers are twice more likely to have an anxiety problem (CI 2.06 2.38) and four times more likely to experience depression (CI 3.97 5.11) than those who spend less than 3 hours. For kids spending 4 hours or more with computers, about 16% of them have some anxiety problems (CI 14.98 17.07), and 11% of them experience depression recently (CI 9.73 11.61). Along with the associations between screen time and diagnoses of anxiety and depression, how frequently a family has meals together also has strong linear relationships with both their children’s screen time and mental health. Children who do not have any meal with their family during the past week are twice more likely to have anxiety and three times more likely to experience depression than children who have meals with their family every day. However, in this study, I could not find any strong associations between the severity of kids’ mental illness and screen time, which leaves the open question, whether screen time directly affects children’s mental health. Read more

Stop worrying and love the black box

Stop worrying and love the black box

In many engineering classes, computational methods are treated with fear, uncertainty, and doubt. At the same time, analytic methods are presented as if they were magic.

I think we should spend more time on computational methods, which means cutting back on analytic methods. But I get a lot of resistance from faculty with a dread fear of black boxes.

They warn me that students have to know how these methods work in order to use them correctly; otherwise they are likely to produce nonsense results and accept them blindly.

And if they let students use computational tools at all, the order of presentation is usually “bottom-up”, that is, a lot of “how it works” before “what it does”, and not much “why you should care”.

In my books and classes, we often got “top-down”, learning to use tools first, and opening the hood only when it’s useful. It’s like learning to drive; knowing about internal combustion engines does not make you a better driver.

But a lot of people don’t like that analogy. Recently one of the good people I follow on Twitter wrote, “No, doing fancy analyses without understanding the basic statistical principles isn’t like driving a car without knowing the mechanics. It’s like driving a car while heavily intoxicated, being in all kinds of accidents without knowing it.”

I replied, “I don’t think there is a general principle here. Sometimes you can use black boxes safely. Sometimes you have to know how they work. Sometimes knowing how they work doesn’t actually help.”

So how do we know which scenario we’re in, and what should we do about it? I suggest the following flow chart:

Many black boxes can be used safely; that is, they produce accurate results over the range of relevant problems. In that case, we should ask whether it (really) helps to know how they work. In Scenario 1, the answer is no; we can stop worrying, stop teaching how it works, and use the time we save to teach more useful things.

Of course, some black boxes have sharp edges. They work when they work, but when they don’t, bad things happen. In that case, we should still ask whether it helps to know how they work. In Scenario 3, the answer is no again. In that case, we have to teach diagnosis: What happens when the black box fails? How can we tell? What can we do about it? Often we can answer these questions without knowing much about how the method works.

But sometimes we can’t, and students really need to open the hood. In that case (Scenario 2 in the diagram) I recommend going top down. Show students methods that solve problems they care about. Start with examples where the methods work, then introduce examples where they break. If the examples are authentic, they motivate students to understand the problems and how to fix them.

With this framework, I can explain more concisely my misgivings about how computational methods are taught:

The engineering curriculum is designed on the assumption that we are always in Scenario 2, but Scenarios 1 and 3 are actually more common.