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In this episode, we're taking many episodes' worth of insights and unpacking an extremely complex and important question--in what ways are we winning the fight against cancer, where might that fight go in the coming decade, and how do we know when we're making progress?  No matter how tricky you might think this problem is to solve, the fact is, once you get in there trying to solve it, it's even trickier than you thought.

A Data Scientist's View of the Fight against Cancer

This episode started out as a discussion of recommendation engines, like Netflix uses to suggest movies.  There's still a lot of that in here.  But a related topic, which is both interesting and important, is how to keep data private in the era of large-scale recommendation engines--what mistakes have been made surrounding supposedly anonymized data, how data ends up de-anonymized, and why it matters for you.

Relevant links:
http://www.netflixprize.com/
http://bits.blogs.nytimes.com/2010/03/12/netflix-cancels-contest-plans-and-settles-suit/?_r=0
http://arxiv.org/PS_cache/cs/pdf/0610/0610105v2.pdf

Recommendation Engines and Privacy

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

You might sometimes find that it's hard to get started doing something, but once you're going, it gets easier.  Turns out machine learning algorithms, and especially recommendation engines, feel the same way.  The more they "know" about a user, like what movies they watch and how they rate them, the better they do at suggesting new movies, which is great until you realize that you have to start somewhere.  The "cold start" problem will be our focus in this episode, both the heuristic solutions that help deal with it and a bit of realism about the importance of skepticism when someone claims a great solution to cold starts.

Relevant links:
http://repository.upenn.edu/cgi/viewcontent.cgi?article=1141&context=cis_papers

The Cold Start Problem

A few months ago, Katie started on a project for the Vice President's Cancer Moonshot surrounding how data can be used to better fight cancer.  The project is all wrapped up now, so we wanted to tell you about how that work went and what changes to cancer data policy were suggested to the Vice President.

See lineardigressions.com for links to the reports discussed on this episode.

Fighting Cancer with Data Science: Followup

Today we are delighted to bring you an interview with Matt Might, computer scientist and medical researcher extraordinaire and architect of President Obama's Precision Medicine Initiative.  As the Obama Administration winds down, we're talking with Matt about the goals and accomplishments of precision medicine (and related projects like the Cancer Moonshot) and what he foresees as the future marriage of data and medicine.  Many thanks to Matt, our friends over at Partially Derivative (hi, Jonathon!) and the White House for arranging this opportunity to chat.  Enjoy!

Data and the Future of Medicine : Interview with Precision Medicine Initiative researcher Matt Might

If one machine learning model is good, are two models better?  In a lot of cases, the answer is yes.  If you build many ok models, and then bring them all together and use them in combination to make your final predictions, you've just created an ensemble model.  It feels a little bit like cheating, like you just got something for nothing, but the results don't like: algorithms like Random Forests and Gradient Boosting Trees (two types of ensemble algorithms) are some of the strongest out-of-the-box algorithms for classic supervised classification problems.  What makes a Random Forest random, and what does it mean to gradient boost a tree?  Have a listen and find out.

Ensemble Algorithms

Say you're looking to use some Bayesian methods to estimate parameters of a system.  You've got the normalization figured out, and the likelihood, but the prior... what should you use for a prior?  Empirical Bayes has an elegant answer: look to your previous experience, and use past measurements as a starting point in your prior.

Scratching your head about some of those terms, and why they matter?  Lucky for you, you're standing in front of a podcast episode that unpacks all of this.

Empirical Bayes

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

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

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.

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Sébastien Dubuis