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 1article 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”

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.

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…”

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”

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

Motivation

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”