Build – Test – Move

First a mea culpa, I have a huge backlog of relatively heavy articles that I really want to add to the blog. But I’ve been busy getting married – congratulations to me – and I didn’t have enough time. I strongly believe in following relatively strict guidelines on writing and editing articles, where I set myself deadlines and avoid over-writing on topics – it is just a blog after all – but for deep insights I do also have a minimum standard that I want to be able to produce before I’m willing to hit the Publish button.

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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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Mathematics and Biology II – Practical considerations

Last month I wrote about the historical world-views of mathematicians and biologists. These articles are part of a planned four part series, in an attempt to first understand and then improve the working relationship between these two key scientific disciplines. This is all a work in progress, so at the end, I will try to take the key learnings from each of the articles and distill them into a single composed article.

This month, I want to discuss the practical considerations why mathematics and biology still don’t work so well together.

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Chronic Fatigue Syndrome

This is an article which I don’t want to write, but I also do. I live my life as if nothing happened. I pretend nothing happened. But the effects on my life both then and since have been enormous.

Where were you when 9/11 happened? I was at my parents’ house in Ireland, preparing for my first day at university. I know this because I’ve told myself the story many times by now. I’ve seen the TV reports so often that I can remember the planes crashing into the towers. Only I can’t. I don’t remember any of it.

I was 19 and at least 6 months of my life are completely missing. I got up most days. I talked with people. I successfully registered for university. I moved into on-campus accommodation. I did sport on rare occasions. I even had a girlfriend for 3 months. But the memories were never formed, or if they were I have never had subsequent access (for the neuroscientists out there: they faded out about 12 months later). Continue reading “Chronic Fatigue Syndrome”

Influences: Steve Grand

One of my favourite games from my childhood was Creatures. I still remember buying it in a large cardboard box and finding the small 3.5″ floppy disk which nestled inside. This was my first experience of two new technologies: virtual worlds and alife.

The game featured little furry creatures (they reminded me of Ewoks, from Star Wars) called Norns. These creatures hatch from eggs. The installation disk, as far as I recall, hosts the simulation environment and the encoding for your first Norn egg. The basic idea was that your Norn would hatch and was supposed to have certain behavioural traits which would make it unique compared to those of your friends. The baby Norn would then wander around the virtual world (a side-on platform type world, with very rich background graphics) and try to interact with a number of the items littering the environment. Continue reading “Influences: Steve Grand”

Mathematics and Biology

Having worked in two traditionally distinct fields, both separately and combining the methods of both, I have more than a few thoughts on what separates these disciplines and how this can be quite detrimental.

As I see it there are two core differences between a mathematical world-view and a biological one: the first is in how knowledge is acquired; and the other is the difference between a dynamical world-view and a static one. What may surprise you is which one is static and which one is dynamic!

Knowledge acquisition

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