Category: Mathematical Modelling

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Why do Trees work better than DNNs on genome data?

This topic occurred to me following my recent talk at a dental conference at Charité Berlin. Upon hearing that I have a strong interest in inference, my fellow keynote mentioned that it drives him crazy that random forests, and similar algorithms, work so much better than DNNs on genomic data. He challenged me to come up with a reason for why this is the case.

I think that I know why. The problem I have is that I suspect that I can never prove it. That issue of not being able to prove things in machine learning is probably an equally interesting topic, for a future article, but here I want to address my theory of why random forests work better than DNNs for analysing genome data.

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Keynote @ Charité Berlin

Apparently, it’s that time again. I just gave my second invited keynote at a conference at Charité Berlin. It was really fun.

The audience were dentists – academic dentists. I confess that I struggled to understand why they thought I would be a good fit for their conference. My previous keynote was at the BIH Digital Health Forum – a much more obviously appropriate audience. But, perhaps strangely, the fit was very good.

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Mathematics and Biology III – Bioinformatics

When I sat down in Summer 2018 to begin my blog one of my goals was to write approximately 5 definitive articles about Mathematics and Biology. So far, I have been pretty hard on the efforts in both fields to come together. I began with a review of the very different world-views inherent in the two subjects – combined with a call to arms for likeminded people to come and help out. I followed this with a more practical consideration of the repertoire of techniques necessary and the career constraints, which actively work against combining these two disciplines. Today I want to consider the shining example of bioinformatics – the one area in which mathematics is clearly being used in biology and which demonstrates a clear career path.

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Influences: John Holland

Sometimes I wait a too long before doing what I really want to do. I’ve postponed writing this article more than once. And this mirrors the fact that I postponed going to visit John H. Holland until I missed my chance.

Very few academics have influenced my thinking as much as John Holland did. We never met, although I did half my graduate studies in Chicago, only 6 hours away from his home in Michigan. He was actually the person I had most wanted to do a PhD with before I figured that the American system wasn’t for me. When he died, in 2015, I missed my final chance.

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Influences: Nate Silver

Nate Silver is most famous in the political world for having correctly predicted the results, on a state-by-state level, of the US presidential election in 2008. That’s back when Obama was first elected president. It’s hard to imagine now, but the idea that Obama would win was only given an outside chance by most commentators at the time.

I find it hard to refer to Nate as anything other than Nate since I’ve been listening to the FiveThirtyEight podcast for so long. We don’t know one another, but he’s become a colleague and mentor who lives inside of my head. The reason he is so important to me is because he has become one of my strongest contemporary influences. His success has given me a roadmap for how to lead my life as a mathematical modeller.

I have been developing a series of articles on Mathematics and Biology (article 1, article 2, more to follow). A common theme in these articles is how a mathematically trained individual finds their place in the modern work environment. We want to pursue our art, we also have professional standards and a lot to contribute, but somehow the connection between our skills and the needs of others are missing. By following Nate’s work, I have at least one strong role model who I can attempt to model. Continue reading “Influences: Nate Silver”

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Fosanis: A Brave New Project

I started working at a new job last week. I am now the Head of Data Science at Fosanis GmbH. We’re a startup in Berlin, two years old, and we provide support services for cancer patients. My task is to personalise the approach.

Think personalised medicine, without the medicine. The content we provide has been professionally curated and has been shown to be beneficial to cancer patients. If you speak German, you can try out the content online right now. We will be launching an App-based implementation in the new year.

I want to then take this to the next level. Patients will be treated as a combination of their statistical attributes and their individual trajectories through the interface. From a technological point-of-view, we will be aping many of the approaches pioneered by Facebook. However, we will try to maximise a much trickier to define Quality of Life metric, rather than page refreshes or time spent on the Wall.

This is a really exciting project. I have been looking for a while to find a project where I can apply behavioural modelling approaches to healthcare goals. In a world of rapidly expanding autoimmune diseases I see this ultimately as the new treatment paradigm. What is especially nice is that, in the space in which we are operating there are no real conflicts of interest. I hope that I don’t look back on that statement as hopelessly naive. My impression is that most people in oncology are really trying to make patients’ lives better.

We will be hiring in the first couple of months of 2019, so if you know any talented biological modellers who might be interested, please tell them to email me their CV.

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Simmunology was…

my first startup. It’s done, we’ve shut it down.

I joined Entrepreneur First‘s initial Berlin cohort in April (2018). Through the process, I very quickly met my cofounder and founded Simmunology Limited. We followed the checkpoints laid down by Entrepreneur First (EF), through founding the company, right up to receiving an initial investment of UK£80,000 in return for 10% of the company. Then, at the end of the kick-off meeting, I told them I wanted to shut it down… Continue reading “Simmunology was…”