John Lees' blog

Pathogens, informatics and modelling at EMBL-EBI

Model flexibility and number of parameters

This post is some thoughts I had after reading ‘Real numbers, data science and chaos: How to fit any dataset with a single parameter’ by Laurent Boué. arXiv:1904.12320 The paper above shows that any dataset can be approximated by the following single-parameter function: $\sin^2 (2^{x \tau} \mathrm{arcsin} \sqrt{\alpha})$ Where $x$ is an integer, $\tau$ is a constant which controls the level of accuracy, and $\alpha$ is a real-valued parameter which is fit to the dataset in question.

Quantify everything, all of the time

I recently read the article by Wu et al in Nature Biotechnology (you can also find similar articles in pretty much all of the Nature journals) which analysed data on participants at some virtual meetings over the past couple of years, and came to the conclusion that ‘Virtual meetings promise to eliminate geographical and administrative barriers and increase accessibility, diversity and inclusivity’. Which sounds great! Of course there are certainly some good things to come out of virtual meetings, and many unresolved issues with in person conferences.

Did 1.27M people die from AMR in 2019?

I would answer ‘I don’t know’. If I was being less trite, I would add that I’m more confident saying that it was between 100k and 10M – whichever way you look at it, vast numbers that are growing larger, and which require action on multiple fronts. The authors of the study ‘Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis’ (also called ’the GRAM study’) have actually attempted to estimate this.

Delete your tweets

Each year I delete all my old tweets. Disadvantages to keeping your old tweets around: No-one reads them. They’re difficult to search through. They’ve probably lost most of their context. You might have changed your mind, or they’ve become outdated. Shitposting is usually a lot less funny in retrospect. Advantages to keeping your old tweets around: The dubious ability to quote tweet an old take/prediction that turned out to be true.

Learning rust as a C++/python programmer (advent of code 2021)

This year I used rust to do advent of code (AoC). I got up to day 17 before Christmas caught up with me, but I hope to come back to the last week at some point soon. Here’s my code so far: https://github.com/johnlees/advent-of-code-2021. I’ve never done any rust programming before, so started off by reading these two pages which got me going fairly quickly: https://fasterthanli.me/articles/a-half-hour-to-learn-rust https://github.com/nrc/r4cppp At the moment I usually code in C++ and python (and increasingly CUDA), though I do know a few other languages to various levels.

Review: Video games 2020-2021

The past couple years have been a great time to play video games. Me in 2020 (and 2021). Of course, it’s always been a great time to play video games, but I’ve never written about them before. Here are some of my favourite games from the past couple of years (in rough ranked order in each of the two categories). Puzzles etc Disco Elysium (mystery) No gameplay to speak of, only a few pre-rendered backgrounds, and lots of clicking and reading text.