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.

Continue reading “Mathematics and Biology II – Practical considerations”

Preprint Announcement – Roving and Unsupervised Bias

This week has been a really big week for me. I finally uploaded the first paper from my time as a postdoc to a pre-print server, called the bioRxiv. I did three major pieces of work, during my time as a postdoc, this is the first and potentially the only, of these, to see the light of day.

I am not usually so tardy in getting work out. I published two papers from my PhD – a record for working with my PhD supervisor – the work for both of which was finished before I ever defended the thesis. My postdoc work was a bit special, I ended up directly proving that the previous work of my collaborators was mistaken. Continue reading “Preprint Announcement – Roving and Unsupervised Bias”

Berlin Tech Scene

It’s 38 degrees celsius in Berlin this week, so I’m going to keep this post relatively short. I chose to move to Berlin four years ago (that’s in 2014) directly following my PhD. I chose this city for a number of reasons, one of which is the apparent burgeoning tech scene. I wanted to do a postdoc in Europe, but I wanted the possibility of not having to move city/country again after the contract ended. At the time, three cities stood out for me: London, Paris and Berlin.

London was my first home abroad; I moved there when I was 17. But the political climate in the UK has been toxic for about 10 years now. I’ve considered moving there many times, and each time I’ve rejected the opportunity. Quelle surprise: Brexit finally happened 2 years ago! Continue reading “Berlin Tech Scene”

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”

AI in Healthcare II

Continued from Part I

Part I of this article appeared last week. In it I introduced the topic of statistical vs biophysical approaches to biological applications. I discussed the huge power of statistical approaches in image analysis and providing decision support services to doctors. I then discussed the 5 major limitations of data-driven approaches when they are applied to biological problems.

I will now continue by looking at biophysical approaches, their pros and cons, and finishing up with a brief introduction to hybrids which attempt to combine these two methods. Continue reading “AI in Healthcare II”

AI in Healthcare I


I live in Berlin, which is fast becoming the tech hub of Europe. Over the past two years we have seen a massive up-tick in the number of healthcare oriented startups, which are receiving funding on the basis of their use of Artificial Intelligence (AI). As somebody who knows a bit about the underlying technical and application problems of AI, what I see has made me very uneasy.

As a result of some personal conversations I was invited to give a Keynote address to the Digital Health Forum of the Berlin Institute of Health in March. This is a big deal because the BIH is a joint venture between Europe’s biggest teaching hospital, Charité Berlin, and one of Germany’s foremost centres for biological research, the Max-Delbrueck-Center, Berlin. The talk was extremely well received, so I have now given a public version at PyData Berlin 2018 which will be published on their YouTube channel in the coming weeks. (Update: the video is available here). In the meantime, I have written the discussion up as an article in two parts: part I is below and part II is available here. Continue reading “AI in Healthcare I”

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”

PyData Berlin 2018

PyData Berlin 2018 will be taking place this weekend. I will be in attendance and, on Saturday, will present a talk on AI in Healthcare.

The abstract I submitted is woefully inadequate. Luckily, I was able to write a more coherent description in the message to the organisers and they were gracious enough to accept me.

I will be talking about my main hobby-topic: why you can’t just throw the current black-box methods at biological problems and expect it to work out.

The talk is the same as one I gave as a keynote in private session at the Digital Health Forum of the Berlin Institute of Health (BIH), in March. The feedback from the BIH was so positive that I wanted to open this topic up to a wider audience (this version will also have a video posted online).

I will write up the talk as an article and post it here in a week or so.

Designing a Disruptive Technology

Did you know that the development of new drugs has been unprofitable since 2005? (article, original study) I knew we were approaching that point, but I didn’t realise that we had already passed the threshold 13 years ago.

I have an insight which will completely disrupt (transform) the pharma industry. I have the background of working in two different domains in order to give credibility to my insight. And I have the ability, on a technical level, to execute on it.

How many of you have heard this pitch before? Continue reading “Designing a Disruptive Technology”