Data science accelerator lesson one- build a pipeline and ship the code!

My exciting news is that I was accepted onto the data science accelerator and have been doing it since late December. My project, basically, is all about using natural language processing to better understand the patient experience data that we collect (and, if I have time, the staff experience data too). Here are the goals:

1) Using an unsupervised technique, generate a novel way of categorising the text data to give us a different perspective. We already have tagged data but I would like to interrogate the usefulness of the tags that we have used
2) a. Generate a system that, given a comment or set of comments, can find other comments within the data that are semantically similar. Note that this system will need to run live on the server, since it would be impossible to store the semantic similarity of every comment to every other comment
3) b. Generate a system that, instead of searching by word, searches by similarity to that word
3) Produce a supervised learning algorithm which can be trained on a sample of tagged comments and then produce tags for comments that it has not previously seen
4) a. Produce a sentiment analysis function that can tag every comment in a database with how positive or negative it is
4) b. Produce reporting functions that can compute overall sentiment for a group of documents (e.g. of a particular service area) and optionally describe the change in sentiment over time

I’m not really sure if I’m going to get through all of it but I’ve made a decent start. I’ve made a Trello board and there’s a GitHub too.

One of the things about the project I haven’t mentioned above is that I want to make something that can easily be picked up and used by other Trusts. There are loads of companies who want to charge money for NHS Trusts to use their black box but I’m trying to make something others can use and build on. So a lot of the work at the end will be on that.

Anyway, I’ll share the work at the end but I’ve learned loads already so I thought I’d talk about that. It’s the best thing I’ve done since my PhD in terms of learning (so I recommend your doing it!) so there are lots of things I want to talk about.

The first one isn’t super complicated or a revelation to anyone but it’s affected the way I work already. It’s this. Ship code! Ship it! Get it out the door!

Up to now to be honest my agile working has pretty much been that I spend six months on something, I release it, it’s terrible, and then I make improvements. One of the product managers at GDS told me that they ship code every week. Every week! I couldn’t believe it. So I’m trying to work like that. Doesn’t matter if it isn’t perfect, doesn’t matter if some of the functionality is reduced, just get something in the hands of your users. Then if they hate it you can avoid spending a month building something they hate.

And, something related to that, start with a pipeline. Right at the start of an analysis, start building the outputs. This helps you to know what all this analysis is actually going to do. It helps you to make the analysis better. And it gives you code that you can ship. Build something that works and does something and give it to your users. They will start giving you feedback before you’ve even finished the analysis. Too often we start with the analysis and only think about the endpoint when we’ve finished. Maybe it’s the wrong analysis. Maybe what you’re doing is clever but no-one cares. Build a pipeline and get it out the door. Let your users tell you what they want.

More on this as the project proceeds

New Year’s post

So this is my annual New Year’s post, it’s an idea from David Allen that I’ve done before.

2018 was the year that I was finally (pretty much) better. I had my bowel and spleen removed in August 2017 and bled in quite a scary way, but by the time 2018 rolled around I was running 9 miles, building mileage ready for a marathon in May. It’s been a great year. I did have some pretty scary health problems (that I won’t go into) but it all worked out in the finish and I’m pretty much back to working and being happy with my family just as I was all the way back in 2014 before everything started to go wrong.

So the first big news of 2018 was I got a new job (March). I’m now half time in my old job, and half time in the new one. They both link together, in that I do Shiny code and server admin to facilitate several dashboards that we use for staff and patient experience and some clinical stuff too. I’m absolutely loving both jobs. We’re doing a lot of stuff that is pretty new in the NHS, we’re the first Trust that I’m aware of with a Shiny Pro licence, and I’ve talked to people all over the country about what we’re doing. My Trust is very supportive and it’s all going really well.

I suppose my next big thing was running a marathon in May. It wasn’t as fast as I would have liked (four hours and thirty three minutes), but I did have quite a few pretty serious problems with being ill so I did pretty well considering. I’ve got another one in 2019, more on which later. Next up was the British Transplant Games (July). It was my first time competing and I won bronze at 5K and 1500m, which was very nice. My big goal now is to qualify for the world games, I’m guessing silver would be enough to do that, partly depends on the time I guess, too.

For the first time in my life I have a savings account, which is absolutely great, and I’m trying (and failing) to save three times my salary by February 2019. My wife and kids are a lot happier now I’m better, we all really went through hell so it’s been a great year just doing normal stuff you can’t do when you’re ill, like go abroad.

And the most recent thing that’s exciting is starting the data science accelerator. I keep meaning to blog more about it, I’m overbusy just doing it, but there’s a GitHub with some of the first steps on here. Text analysis is really easy to do, and really hard to do well, so I’m really glad that I’ve got a mentor to guide me through it. I’m working really hard trying to build some robust analysis and hopefully deploy some sort of reusable pipeline that other NHS Trusts can use. I’ve been dabbling in Python, too, which I really want to do more of. I feel like having other languages could help me build more and better stuff more easily. I’ve really bought into the whole agile development thing, as well, that’s a part of the accelerator, and one of the talks by a product manager was fascinating.

So that’s it for 2018. I’m starting 2019 strong. Very strong. My health was a teensy bit wobbly this time last year but I’m as strong as an ox at the moment. It really feels good after being frightened and weak for such a long time. At work I want to tie up all the threads and be a part of an agile data science team, producing robust statistical analyses using interactive web based technologies (like Shiny!).

Oh yes! That reminds me. Of course last year I also wrote a book and I started teaching statistics to Trust staff- advanced stuff in 12 one hour tutorials and a quick review in a 2 and a half hour lecture. The teaching has been going really well, I’ve been getting a lot of good feedback and I’m really hoping it helps my Trust do better with the data it collects.

I live a blessed life. All I want to do in 2019 is keep doing the same stuff I already do and love. Run a faster marathon (sub 4 hour). Get a silver medal. Be part of a bigger, better data science team. Keep doing all the stuff we’re doing with Shiny and text analysis and help other Trusts to do it, too. And more than anything else I want my family to just live a normal life and forget about all that stuff between 2015-2017.

Oh yeah. And I want to solve the Rubik’s cube, too. My eldest got one for Christmas and it’s got me hooked.

That’s me for 2019. Good luck with whatever you’ve got on your plate for the year 🙂