Building a pulse oximeter

At-home pulse oximeters, those fingertip devices doctors use to measure the oxygen saturation in your blood, have been selling out everywhere thanks to the Covid-19 pandemic.

But as my Quartz colleague Amirta Khalid points out in this great article, most people don't need 'em. If your oxygen level is worryingly low, you'll know — you don't need a machine to tell you. Folks with some existing conditions, however, can use a pulse oximeter to help a remote doctor monitor their vitals or to adjust supplementary oxygen devices.

When Khalid mentioned she was working the story, it reminded me of the DIY "pulse ox" sensor Sparkfun sells. It, like other pulse oximeters, shines light into the skin and makes measurements based on how that light is absorbed. I've built heartbeat-driven projects before and had been exploring new ways to monitor pulse rates. So I got one.

Sparkfun warns in red letters that "this device is not intended to diagnose or treat any conditions," and I offer the same caution if you're tempted to build one. The process wasn't hard at all. I got it running quickly ... and then added an LED display for fun and flourish.

Here's how I made it, and the code, too.

Work-from-home "on air" light

I'm incredibly lucky to be both healthy and able to work from home during this coronavirus crisis. That means I spend large chunks of my day on video calls.

As a courtesy to my family, all of whom are also working and schooling from home, I've tried to warn them when they risk being broadcast to my colleagues. 

Now I have a fun "on air" light to help! And I've put the code online so you can make one, too.

DIY aquarium lights

Buy a new aquarium, and you often get hood lights that are ... meh. They're good enough, but not great.

There are plenty of high-quality replacement lights out there, but none of them had the nice, low profile of the plastic covers that came with this tank. So I decided to spruce up the existing illumination with some DYI lights — and even make them programmable with an Arduino.

That was more than a year ago. Now in coronavirus isolation, I finally made it happen.

Here's how.

Amazon Aurora MySQL + Python

Ok, so this isn't the sexiest topic, but if you're completely stuck the way I was several times today, maybe you're happy you found this post.

Today I needed to spin up a database I want available to students at the Newmark Graduate School of Journalism and also colleagues at Quartz. I also want to connect to the database from my home and the school using Python.

Since we use Amazon's web services, and I wanted to show the students SQL, I decided to give the AWS Aurora system a whirl — specifically the MySQL-compatible version.

As with many things AWS, it was a bit of a slog to get set up ... and I've decided to jot it all down while it's fresh so I can remember how the heck I did it (and show my students).

After a few tries, here's how I finally got set up:

Machine learning in my pajamas

Tonight I gave a presentation at Newsgeist about how I did machine learning in my pajamas — in my pajamas.

I promised the gathered crowd I'd post how they, too, can make their own bike-detector, so here it goes:

  1. Follow the instructions here.
  2. When you get to the part about picking a notebook, use this one: notebooks/ee-searching-videos-with-fastai.ipynb

Then follow the steps to work through the code! Have fun!

AI classes for journalists

(Promo video for the Knight Center course.)

If you're a journalist, you've probably done a story or two about about AI.  But did you know you can use machine learning, too? 

I'll show you! 

While the classes below have passed, the videos and accompanying code for the Knight Center course are now available free online.

Work at your own pace and enjoy. It could help with your next investigation, and the experience will help you report about machine learning, too.

Past classes:

September 13, 2019 • 11 am •  InterContinental New Orleans • Treme / 2nd Floor 

Hands-on Introduction: Machine Learning for Journalists at ONA

If you're going to ONA, get a practical, hands-on introduction to using machine learning to help pore through documents, images, and data records. This 90-minute training session by members of the Quartz AI Studio will give you the chance to use third-party tools and learn how to make custom machine-learning models. We'll walk you through pre-written code you can take home to your newsroom.

October 26 & 27, 2019 • Newmark Graduate School of Journalism • New York City

This will be a small-group, guided bootcamp where we'll spend the weekend working through practical machine-learning solutions for journalists. You'll learn to recognize cases when machine learning might help solve such reporting problems, to use existing and custom-made tools to tackle real-world issues, and to identify and avoid bias and error in your work. Students will get personalized instruction and hands-on experience for using these methods on any beat.

November 18 to December 15 • Knight Center for Journalism in the Americas • Online • $95

4-Week Online Course: Hands-on Machine Learning Solutions for Journalists

In this online video course, you will first learn how to use some off-the-shelf systems to get fast answers to basic questions: What’s in all of these images? What are these documents about? Then we’ll move to building custom machine learning models to help with a particular project, such as sorting documents into particular piles. Our work will be done with pre-written code, so you always start with a working base. You’ll then learn more by modifying it.

Updated 21 April 2020

Detecting feature importance in neural networks

I'm working on a new neural network that tries to predict an outcome – true or false – based on 65 different variables in a table.

The tabular model I made with is somewhat accurate at making those predictions (it's a small data set of just 5,000 rows). But to me even more interesting is determining which of the 65 features matter most. 

I knew calculating this "feature importance" was possible with random forests, but could I do it with neural nets?

It turns out I can. The trick is, essentially, to try the model without each feature. The degree to which the model gets worse with that feature missing indicates its importance – or lack of importance.

This blog post describes how to run this test, and this adaptation worked perfectly in my notebook. Here's the code in a Gist:

Unfortunately, because my project uses internal Quartz analytics, I can't share the data or the charts I'm playing with. But with the code above, I can now "see into" the neural network and get cool insights about what's going on

Converting videos to images for machine learning

This week I kept to my summer of training plan, however the model-building I did was for a Quartz project we're not ready to share. But! I learned something super useful in the process: how to quickly turn videos into many still images.

For our latest project, I'm training a model to identify specific objects available to me – much like how I trained a model to identify items in the office.

The fastest way to get lots of images of an object is to take a video of it. And a quick way to turn that video into images – called an "image sequence" – is ffmpeg. It seems to convert from many formats like .mp4, .mov, .avi to lots different image formats such as .jpg and .png.

There's plenty more detail in the ffmpeg docs, but here's what I did that worked so quickly on my Mac:

brew install ffmpeg

I use Homebrew to put things on my Mac, so this went pretty quickly. I had to update my Xcode command line tools, but Homebrew is super helpful and told me exactly what I needed to do.

Next, I did this from the Terminal:

ffmpeg -i IMG_1019.MOV -r 15 coolname%04d.jpg

Here's what's going on:

  • -i means the next thing is the input file
  • IMG_1019.MOV is the movie I Airdropped from my phone to my laptop
  • -r is the flag for the sample rate.
  • 15 is the rate. I wanted every other image, so 15 frames every second. 1 would be every second; 0.25 every 4th second.
  • coolname is just a prefix I picked for each image
  • %04d means each frame gets a zero-padded sequence number, starting with 0001 and going to 9999– so my image files are named coolname0001.jpg, coolname0002.jpg, coolname0003.jpg, etc.
  • .jpg is the image format I want. If I put .png I got PNGs instead.

In mere moments I had a dozens of JPG files I could use for training. And that's pretty great.

Artisanal AI: Detecting objects in our office

Off-the-shelf services like the Google Vision are trained to identify objects in general, like car, vehicle, and road in the image below.

But many of the journalism projects we're encountering in the Quartz AI Studio benefit from custom-built models that identify very specific items. I recently heard Meredith Broussard call this kind of work "artisanal AI," which cracked me up and also fits nicely.

So as an experiment, and as part of my summer training program, I trained an artisanal model to identify between the three objects at the top of this page from the Quartz offices: A Bevi water dispenser, a coffee urn, and a Quartz Creative arcade game (don't you wish you had one of those?!)

I also made a little website where my colleagues and I can test the model. You can, too — though you'll have to come visit to get the best experience!

The results

The model is 100% accurate at identifying the images I fed it — which probably is not all that surprising. It's based on an existing model called resnet34, which was trained on the ImageNet data set to distinguish between thousands of things. Using a technique called transfer learning, I taught that base model to use all of its existing power to distinguish between just three objects.

Making music with my arms

The brilliant Imogen Heap performed in New York a few weeks ago, and I got to experience live how she crafts sounds with her arms and hands

It was a great night of beautiful music and technology, both.

One mystery I couldn't solve from the audience was how her computer detected the position of her arms. Unlike in her early videos, I didn't see something akin to a Kinect on stage.

Now I think maybe I know.

That's because this week I took a workshop from Hannah Davis on using the ml5.js coding library, which touts itself as "friendly machine learning for the web," letting me use machine learning models in a browser. The class was part of the art+tech Eyeo Festival in Minneapolis.

One of the models Davis demonstrated was PoseNet (also here), which estimates the position of various body parts — elbows, wrists, knees, etc — in an image or video. I'd never seen PoseNet work before, let alone in JavaScript and in a browser.

Inspired by Heap, I set out to quickly code a music controller based on my arm movements, as seen by PoseNet through my laptop camera.

Try it yourself

It's pretty rough, but you can try it here. Just let the site use your camera, toggle the sound on, and try controlling the pitch by moving your right hand up and down in the camera frame!

I put it on Glitch, which means you can remix it. Or take a peek at the code on Github.

There are lots more ml5.js examples you can try. Just put the index.html, script.js, and models (if there's such a folder) someplace on the web where the files can be hosted. Or put them on your local machine and run a simple "localhost" server.