Invited Speaker: Dynamics of Immune Responses

I have been invited to speak at the Dynamics of Immune Responses workshop/seminar/conference in May-June 2020. The invitation arose through my previous efforts to found a company in this space.

There is a growing awareness in the field of immunology of the potential for using mathematical techniques. The wedge-issue here is the cascade of data appearing via new cytometry techniques; large-data looks like a math issue to most people. I of course come from the other side of a spectrum – everything looks like a math issue to me – I wanted to stimulate drug development which engages with immune system dynamics by founding my company.

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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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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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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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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.

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