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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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The network you grow up with

A sense of home is a powerful feeling. The sense of belonging, of knowing where everything is. I miss that sometimes.

I left Ireland almost exactly 10 years ago with a burning need to go out and prove myself. I had finally recovered from Chronic Fatigue Syndrome and was going to take up a much delayed PhD position. I moved to the University of Luebeck, where I found my introduction to neuroscience, before moving on to Paris Descartes, the École Normale Supérieure and the University of Chicago. With each move I developed a new network of colleagues, collaborators, and mentors.

A couple of weeks ago I was contacted by a member of the Irish mathematical community. Many years ago I wrote the website for the Mathematics Department at NUI, Galway. While doing that I included biographies of the then members of staff and their research domains. At some point, I also made a backup of the website for my own reference under my personal domain. Sadly, many of the members of staff who worked at NUI, Galway when I was an undergraduate are now dead. So now this resource has become a useful archive. And thus I was re-discovered by a member of the current Irish mathematical community.

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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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One year-a blogging

One year ago I finally picked up the courage to put my thoughts publicly online. I led with a traditional Hello World but I quickly followed-up with my opening manifesto for the company I was trying to establish Simmunology.

The discipline of writing is something I initially discovered, when I first moved to Germany, 10 years ago. It clarifies my thoughts and allows me to discover the holes in my own thinking.

Blogging has paid off immensely. Before, I was afraid of sharing my thoughts and having my opinions come back to bite me. This sometimes led me to go too far down paths that I didn’t agree with.

Eventually I had to accept that I have accumulated considerable life experience. And that those to whom I was listening had typically less things of importance to say than I do. Finally, if I put it here and you disagree with me – I might change my mind – it will certainly lead to a more aligned working relationship.

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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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Entrepreneur First the Index VC Fund

I took part in Entrepreneur First’s (EF’s) first Berlin cohort last summer. I have largely refrained from talking about my experience, even in private so far, but this hasn’t prevented a lot of people from giving me their opinions on the business model of EF.

The EF hypothesis sounds simple: get enough smart and motivated people together in a cohort and give them the opportunity (time, access to funds, etc.) to start businesses together and some of them will succeed…. bigly.

The venture capital community here in Berlin are not so convinced. Personally I sympathise with their doubts. Certainly from an operations point of view, scaling EF has seen problems. However, as a business model it may be genius.

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