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Machine learning and particle physics go together like peanut butter and jelly--but this is a relatively new development.  

For many decades, physicists looked through their fairly large datasets using the laws of physics to guide their exploration; that tradition continues today, but as ever-larger datasets get made, machine learning becomes a more tractable way to deal with the deluge.  

With this in mind, ATLAS (one of the major experiments at CERN, the European Center for Nuclear Research and home laboratory of the recently discovered Higgs boson) ran a machine learning contest over the summer, to see what advances could be found from opening up the dataset to non-physicists.  

The results were impressive--physicists are smart folks, but there’s clearly lots of advances yet to make as machine learning and physics learn from one another.  And who knows--maybe more Nobel prizes to win as well!

https://www.kaggle.com/c/higgs-boson

Hunting for the Higgs

In the 1850s, there were a lot of things we didn’t know yet: how to create an airplane, how to split an atom, or how to control the spread of a common but deadly disease: cholera.  

When a cholera outbreak in London killed scores of people, a doctor named John Snow used it as a chance to study whether the cause might be very small organisms that were spreading through the water supply (the prevailing theory at the time was miasma, or “bad air”).  By tracing the geography of all the deaths from the outbreak, Snow was practicing elementary data science--and stumbled upon one of history’s most famous outliers.  

In this episode, we’ll tell you more about this single data point, a case of cholera that cracked the case wide open for Snow and provided critical validation for the germ theory of disease.

http://en.wikipedia.org/wiki/1854_Broad_Street_cholera_outbreak

How Outliers Helped Defeat Cholera

Computers are capable of many impressive feats, but making you laugh is usually not one of them. Or could it be? This episode will talk about a custom-built machine learning algorithm that searches through text and writes jokes based on what it finds. 

The jokes are formulaic: they're all of the form "I like my X like I like my Y: Z" where X and Y are nouns, and Z is an adjective that can describe both X and Y. For (dumb) example, "I like my men like I like my coffee: steaming hot." The joke is funny when ZX and ZY are both very common phrases, but X and Y are rarely seen together. 

So, given a large enough corpus of text, the algorithm looks for triplets of words that fit this description and writes jokes based on them. Are the jokes funny? You be the judge...

http://homepages.inf.ed.ac.uk/s0894589/petrovic13unsupervised.pdf

Computers Try to Tell Jokes

Baseball is characterized by a high level of equality between teams; even the best teams might only have 55% win percentages (contrast this with college football, where teams go undefeated pretty regularly). In this regime, where 2 outcomes (Giants win/Giants lose) are approximately equally likely, we can model the win/loss chances with a binomial distribution. 

Using the binomial distribution, we can calculate an interesting little result: what's the chance of the world series going to only 4 games? 5? 6? All the way to 7? Then we can compare to decades' worth of world series data, to see how well the data follows the binomial assumption. 

The result tells us a lot about sports psychology--if each game is independent of the others, 4/5/6/7 game series are equally likely. The data shows a different trend: 4 and 7 game series are significantly more likely than 5 or 6. There's a powerful psychological effect at play--everybody loves the 7th game of the world series, or a good sweep. And it turns out that the baseball teams, whether they intend it or not, oblige our love of short (4) and long (7) world series!

http://blog.philbirnbaum.com/2007/06/winning-world-series-in-x-games.html

Stats of World Series Streaks

A true classic topic in ML: Facial recognition is very high-dimensional, meaning that each picture can have millions of pixels, each of which can be a single feature. It's computationally expensive to deal with all these features, and invites overfitting problems. PCA (principal components analysis) is a classic dimensionality reduction tool that compresses these many dimensions into the few that contain the most variation in the data, and those principal components are often then fed into a classic ML algorithm like and SVM. 

One of the best thing about eigenfaces is the great example code that you can find in sklearn--you can distinguish pictures of world leaders yourself in just a few minutes!

http://scikit-learn.org/stable/auto_examples/applications/face_recognition.html

Facial Recognition with Eigenfaces

Ever feel like you could randomly assemble words from a certain vocabulary and make semi-coherent Kanye West lyrics? Or technical documentation, imitations of local newscasters, your politically outspoken uncle, etc.? Wonder no more, there's a way to do this exact type of thing: it's called a Markov Chain, and probably the most powerful way to generate made-up data that you can then use for fun and profit. The idea behind a Markov Chain is that you probabilistically generate a sequence of steps, numbers, words, etc. where each next step/number/word depends only on the previous one, which makes it fast and efficient to computationally generate. Usually Markov Chains are used for serious academic uses, but this ain't one of them: here they're used to randomly generate rap lyrics based on Kanye West lyrics.

Random Kanye

Wikipedia says, "A hidden Markov model (HMM) is a statistical Markov model in which the system being modeled is assumed to be a Markov process with unobserved (hidden) states." What does that even mean?

In part one of a special two-parter on HMMs, Katie, Ben, and special guest Francesco explain the basics of HMMs, and some simple applications of them in the real world. This episode sets the stage for part two, where we explore the use of HMMs in Modern Genetics, and possibly Katie's "Um Detector."

Introducing Hidden Markov Models (HMM Part 1)

In part two of our series on Hidden Markov Models (HMMs), we talk to Katie and special guest Francesco about more useful and novel applications of HMMs. We revisit Katie's "Um Detector," and hear about how HMMs are used in genetics research.

Genetics and Um Detection (HMM Part 2)

After the Challenger exploded in 1986, killing all 7 astronauts aboard, an investigation into the cause was immediately launched. 

In the cold temperatures the night before the launch, the o-rings that seal off the fuel tanks from the rocket boosters became inflexible, so they did not seal properly, which led to the fuel tank explosion. NASA knew that there could be o-ring problems, but performed the analysis of their data incorrectly and ended up massively underestimating the risk associated with the cold temperatures. 

In this episode, we'll unpack the mistakes they made. We'll talk about how they excluded data points that they thought were irrelevant but which actually were critical to recognizing a fatal pattern.

Statistical Mistakes and the Challenger Disaster

There is no known learning algorithm that is more flexible and powerful than the human brain. That's quite inspirational, if you think about it--to level up machine learning, maybe we should be going back to biology and letting millions of year of evolution guide the structure of our algorithms. 

This is the idea behind neural nets, which mock up the structure of the brain and are some of the most studied and powerful algorithms out there. In this episode, we’ll lay out the building blocks of the neural net (called neurons, naturally) and the networks that are built out of them. 

We’ll also explore the results that neural nets get when used to do object recognition in photographs.

Neural Nets (Part 1)

Come get a little "out there" with us this week, as we use a meta-study of extrasensory perception (or ESP, often used in the same sentence as "psychics") to chat about Bayesian vs. frequentist statistics.

Bayesian Psychics

This machine learning algorithm beat the human champions at Jeopardy.  What is... Watson?

Watson

Doing some science, and want to know if you might have found something?  Or maybe you've just accomplished the scientific equivalent of going fishing and reeling in an old boot?  Frequentist p-values can help you distinguish between "eh" and "oooh interesting".  Also, there's a lot of physics in this episode, nerds.

PFun with P Values

Building a machine learning system and maintaining it in production are two very different things. Some folks over at Google wrote a paper that shares their thoughts around all the items you might want to test or check for your production ML system.

Relevant links:
https://research.google.com/pubs/pub45742.html

Defining the quality of a machine learning production system

Autoencoders are neural nets that are optimized for creating outputs that... look like the inputs to the network. Turns out this is a not-too-shabby way to do unsupervised machine learning with neural nets.

Autoencoders

Convolutional nets are great for image classification... if this were 2016. But it's 2018 and Canada's greatest neural networker Geoff Hinton has some new ideas, namely capsule networks. Capsule nets are a completely new type of neural net architecture designed to do image classification on far fewer training cases than convolutional nets, and they're posting results that are competitive with much more mature technologies.

In this episode, we'll give a light conceptual introduction to capsule nets and get geared up for a future episode that will do a deeper technical dive.

A Conceptual Introduction to Capsule Networks

Last episode we talked conceptually about capsule networks, the latest and greatest computer vision innovation to come out of Geoff Hinton's lab. This week we're getting a little more into the technical details, for those of you ready to have your mind stretched.

A Technical Introduction to Capsule Networks

A huge part of the ascent of deep learning in the last few years is related to advances in computer hardware that makes it possible to do the computational heavy lifting required to build models with thousands or even millions of tunable parameters. This week we'll pretend to be electrical engineers and talk about how modern machine learning is enabled by hardware.

CPUs, GPUs, TPUs: Hardware for Deep Learning

As machine learning models get into the hands of more and more users, there's an increasing expectation that black box isn't good enough: users want to understand why the model made a given prediction, not just what the prediction itself is. This is motivating a lot of work into feature important and model interpretability tools, and one of the most exciting new ones is based on Shapley Values from game theory. In this episode, we'll explain what Shapley Values are and how they make a cool approach to feature importance for machine learning.

Game Theory for Model Interpretability: Shapley Values

Shapley values in machine learning are an interesting and useful enough innovation that we figured hey, why not do a two-parter? Our last episode focused on explaining what Shapley values are: they define a way of assigning credit for outcomes across several contributors, originally to understand how impactful different actors are in building coalitions (hence the game theory background) but now they're being cross-purposed for quantifying feature importance in machine learning models. This episode centers on the computational details that allow Shapley values to be approximated quickly, and a new package called SHAP that makes all this innovation accessible.

SHAP: Shapley Values in Machine Learning

If you're a data scientist, chances are good that you've heard of git, which is a system for version controlling code. Chances are also good that you're not quite as up on git as you want to be--git has a strong following among software engineers but, in our anecdotal experience, data scientists are less likely to know how to use this powerful tool. Never fear: in this episode we'll talk through some of the basics, and what does (and doesn't) translate from version control for regular software to version control for data science software.

Git for Data Scientists

If you've been in data science for more than a year or two, chances are you've noticed changes in the field as it's grown and matured. And if you're newer to the field, you may feel like there's a disconnect between lots of different stories about what data scientists should know, or do, or expect from their job. This week, we cover two thought pieces, one that arose from interviews with 35(!) data scientists speaking about what their jobs actually are (and aren't), and one from the head of data science at AirBnb organizing core data science work into three main specialties.

Relevant links:
https://hbr.org/2018/08/what-data-scientists-really-do-according-to-35-data-scientists
https://www.linkedin.com/pulse/one-data-science-job-doesnt-fit-all-elena-grewal

The Three Types of Data Scientists, and What They Actually Do

If you’re a data scientist, you know how important it is to keep your data orderly, clean, moving smoothly between different systems, well-documented… there’s a ton of work that goes into building and maintaining databases and data pipelines. This job, that of owner and maintainer of the data being used for analytics, is often the realm of data engineers. From data extraction, transform and loading procedures to the data storage strategy and even the definitions of key data quantities that serve as focal points for a whole organization, data engineers keep the plumbing of data analytics running smoothly.

Data Engineering

Open source software is ubiquitous throughout data science, and enables the work of nearly every data scientist in some way or another. Open source projects, however, are disproportionately maintained by a small number of individuals, some of whom are institutionally supported, but many of whom do this maintenance on a purely volunteer basis. The health of the data science ecosystem depends on the support of open source projects, on an individual and institutional level.

https://hdsr.mitpress.mit.edu/pub/xsrt4zs2/release/2

The Data Science Open Source Ecosystem

This is a re-release of an episode that originally ran in October 2019.

If you’re trying to manage a project that serves up analytics data for a few very distinct uses, you’d be wise to consider having custom solutions for each use case that are optimized for the needs and constraints of that use cases. You also wouldn’t be YouTube, which found themselves with this problem (gigantic data needs and several very different use cases of what they needed to do with that data) and went a different way: they built one analytics data system to serve them all. Procella, the system they built, is the topic of our episode today: by deconstructing the system, we dig into the four motivating uses of this system, the complexity they had to introduce to service all four uses simultaneously, and the impressive engineering that has to go into building something that “just works.”

Procella: YouTube's super-system for analytics data storage

A few weeks ago, we put out a call for data scientists interested in issues of race and racism, or people studying how those topics can be studied with data science methods, should get in touch to come talk to our audience about their work. This week we’re excited to bring on Todd Hendricks, Bay Area data scientist and a volunteer who reached out to tell us about his studies with the Stanford Open Policing dataset.

A Data Science Take on Open Policing Data

The data science and artificial intelligence community has made amazing strides in the past few years to algorithmically automate portions of the healthcare process. This episode looks at two computer vision algorithms, one that diagnoses diabetic retinopathy and another that classifies liver cancer, and asks the question—are patients now getting better care, and achieving better outcomes, with these algorithms in the mix? The answer isn’t no, exactly, but it’s not a resounding yes, because these algorithms interact with a very complex system (the healthcare system) and other shortcomings of that system are proving hard to automate away. Getting a faster diagnosis from an image might not be an improvement if the image is now harder to capture (because of strict data quality requirements associated with the algorithm that wouldn’t stop a human doing the same job). Likewise, an algorithm getting a prediction mostly correct might not be an overall benefit if it introduces more dramatic failures when the prediction happens to be wrong. For every data scientist whose work is deployed into some kind of product, and is being used to solve real-world problems, these papers underscore how important and difficult it is to consider all the context around those problems.

A Reality Check on AI-Driven Medical Assistants

All good things must come to an end, including this podcast. This is the last episode we plan to release, and it doesn’t cover data science—it’s mostly reminiscing, thanking our wonderful audience (that’s you!), and marveling at how this thing that started out as a side project grew into a huge part of our lives for over 5 years.

It’s been a ride, and a real pleasure and privilege to talk to you each week. Thanks, best wishes, and good night!

—Katie and Ben