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Genomics data is some of the biggest #bigdata, and doing machine learning on it is unlocking new ways of thinking about evolution, genomic diseases like cancer, and what really makes each of us different for everyone else.  This episode touches on some of the things that make machine learning on genomics data so challenging, and the algorithms designed to do it anyway.

Machine Learning for Genomics

What do you get when you cross a support vector machine with matrix factorization?  You get a factorization machine, and a darn fine algorithm for recommendation engines.

Factorization Machines

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

Linear regression is a great tool if you want to make predictions about the mean value that an outcome will have given certain values for the inputs. But what if you want to predict the median? Or the 10th percentile? Or the 90th percentile. You need quantile regression, which is similar to ordinary least squares regression in some ways but with some really interesting twists that make it unique. This week, we’ll go over the concept of quantile regression, and also a bit about how it works and when you might use it.

Relevant links:
https://www.aeaweb.org/articles?id=10.1257/jep.15.4.143
https://eng.uber.com/analyzing-experiment-outcomes/

Quantile Regression

It’s not news that data scientists are expected to be capable in many different areas (writing software, designing experiments, analyzing data, talking to non-technical stakeholders). One thing that has been changing, though, as the field becomes a bit older and more mature, is our ideas about what data scientists should focus on to stay relevant. Should they specialize in a particular area (if so, which one)? Should they instead stay general and work across many different areas? In either case, what are the costs and benefits?

This question has prompted a number of think pieces lately, which are sometimes advocating for specializing, and sometimes pointing out the benefits of generalists. In short, if you’re trying to figure out what to actually do, you might be hearing some conflicting opinions. In this episode, we break apart the arguments both ways, and maybe (hopefully?) reach a little resolution about where to go from here.

The Great Data Science Specialist vs. Generalist Debate

We often hear from folks wondering what advice we can give them as they search for their first job in data science. What does a hiring manager look for? Should someone focus on taking classes online, doing a bootcamp, reading books, something else? How can they stand out in a crowd? 

There’s no single answer, because so much depends on the person asking in the first place, but that doesn’t stop us from giving some perspective. So in this episode we’re sharing that advice out more widely, so hopefully more of you can benefit from it.

Advice to those trying to get a first job in data science

This is a re-release of an episode that originally aired on April 1, 2018

If you've done image recognition or computer vision tasks with a neural network, you've probably used a convolutional neural net. This episode is all about the architecture and implementation details of convolutional networks, and the tricks that make them so good at image tasks.

Convolutional Neural Networks

A message from Ben around algorithmic bias, and how our models are sometimes reflections of ourselves.

An interstitial word from Ben

As protests sweep across the United States in the wake of the killing of George Floyd by a Minneapolis police officer, we take a moment to dig into one of the ways that data science perpetuates and amplifies racism in the American criminal justice system. COMPAS is an algorithm that claims to give a prediction about the likelihood of an offender to re-offend if released, based on the attributes of the individual, and guess what: it shows disparities in the predictions for black and white offenders that would nudge judges toward giving harsher sentences to black individuals. 

We dig into this algorithm a little more deeply, unpacking how different metrics give different pictures into the “fairness” of the predictions and what is causing its racially disparate output (to wit: race is explicitly not an input to the algorithm, and yet the algorithm gives outputs that correlate with race—what gives?) Unfortunately it’s not an open-and-shut case of a tuning parameter being off, or the wrong metric being used: instead the biases in the justice system itself are being captured in the algorithm outputs, in such a way that a self-fulfilling prophecy of harsher treatment for black defendants is all but guaranteed. Like many other things this week, this episode left us thinking about bigger, systemic issues, and why it’s proven so hard for years to fix what’s broken.

Racism, the criminal justice system, and data science

This episode features Zach Drake, a working data scientist and PhD candidate in the Criminology, Law and Society program at George Mason University. Zach specializes in bringing data science methods to studies of criminal behavior, and got in touch after our last episode (about racially complicated recidivism algorithms). Our conversation covers a wide range of topics—common misconceptions around race and crime statistics, how methodologically-driven criminology scholars think about building crime prediction models, and how to think about policy changes when we don’t have a complete understanding of cause and effect in criminology. For the many of us currently re-thinking race and criminal justice, but wanting to be data-driven about it, this conversation with Zach is a must-listen.

Criminology and Data Science

This is a re-release of an episode that first ran on January 29, 2017.

This  week: everybody's favorite WWII-era classifier metric!  But it's not  just for winning wars, it's a fantastic go-to metric for all your  classifier quality needs.

Rock the ROC Curve

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

Machine Learning for Genomics

Linear Digressions

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