Category: Health Biology

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Mathematics and Biology (the Pharma Vision)

I began this blog almost exactly three years ago. My goal was two-fold: first, to demonstrate thought leadership in an area in which I was then founding a company; and, second, to have a demonstrated track-record rather than a picture-perfect pitch-deck. This latter is clearly a sub-goal of the first.

In those early days, I began a series of articles on Mathematics and Biology. I began with a comparison of the two fields. From there I moved on to discussing the people and skills involved, essentially why mathematicians so rarely do biology. I then discussed the outlier which is bioinformatics. I had two further articles planned in the series, after which point I wanted to attempt a synthesis. The missing articles are on the Microbiome and Quantitative Systems Pharmacology (QSP). These will remain missing articles for now, time has moved on and my thoughts on all of these topics have progressed enormously.

A few weeks ago I published a futurecast about using virtual patient’s for pharma drug development. There was a key idea buried in that article which in essence is my current synthesis perspective on mathematics and biology. I want to highlight this idea here and flesh it out slightly.

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Three things I know: Future-casting 2 of 3

Last week I published an article about Artificial General Intelligence. This week I want to follow-up with my second of three attempts to predict the future. As I said, last week, this was part of a game which is commonly played in incubators when trying to draw insights from deep-tech founders. This week I want to talk about the Virtual Patient for drug development

I founded my first company over three years ago. We made no secret of our interest in using in-silico methods to build a Virtual Patient for drug development. We didn’t succeed that time but our lack of success had little to do with either technical issues or a lack of a commercialisation option, it was entirely our own fault.

The Virtual Patient

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New article: My experience of the BIA Pulse accelerator

I wrote recently about my experiences of the Pulse leadership and entrepreneurship training program for the blog of the UK BioIndustry Association (BIA). The Pulse course is organised jointly by the BIA and the Francis Crick Institute. I joined the three-day course, in its first year of operation, in 2018.

I felt that I benefited enormously from the course. I had left my postdoc position 3 months previously and I was researching ideas for setting-up a company. I subsequently took my learnings from Pulse and elsewhere, and established my first company Simmunology. So when I was contacted earlier this year I was particularly keen to write something and say thanks.

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Modelling the Modeller

Something I’ve struggled with on and off over the 20 years that I have been making mathematical models is explaining those models to others. I have tried to bring people along and develop their understanding. But mainly what I observed was that, some people just got it and others did not.

I have certainly improved my own skill at explaining. This comes down to having streamlined stories and simpler take-home messages. Telling a clearer story certainly improves my audiences’ self-satisfaction, but ultimately some of them get the whole message and others do not.

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Narrative and Decision Models

Since I managed to break my writers’ block on decision making models last week I want to follow-up with a brief discussion on the use of Narrative in presenting decision models to an audience.

In my first article on decision making models I emphasized that a model must serve a purpose. In explaining our models to others I want to highlight that there are two purposes behind explaining a model; the first is to convince the audience; the second is to convey insights into the model. This is the opposite ordering of how scientifically-trained modellers typically think about communicating results, but it is by far-and-away the prioritisation of most top scientific communicators around the world.

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Decision Making Using Models 3.0

This is my third attempt, over the course of 9 months, to write this article. The first attempt foundered on my desire to go into detail on whether explanation or explanability is a good characteristic of a model or not. I confess, this was overly motivated by my personal frustration at having worked with somebody who, “never let the facts get in the way of a good story.” The second attempt got lost in a forest of anecdotes from previous projects. I was trying so hard to knit them together that I failed to make a point. Today, I want to focus on the single most important thing that I have learned about developing decision making models.

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Talks cancelled – Talks online

I had quite a nice spring season of talks planned for 2020. I was invited to deliver a keynote on AI in Healthcare at Biovaria. And, I was one of the invited speakers for the Dynamics of Immune Repertoires conference where I would also have given a workshop, in Dresden. Covid-19 struck and the rest is history.

Emergencies lead to quick changes of plans. Anthony Kelly from AI in Action reached out to me asking me to take part in a special on AI in Healthcare.

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Data Science in Biomedical Industry

I am asked quite often how I see Data Science in the biomedical industry. I have, of course, many answers each of which is context dependent. However one theme which I find frequently recurring is a sort of straw-man debate which seems to inherently attract technical practitioners.

The debate is usually structured as follows:
How do you see the validation of medical AI products working in practice?
Answer: clinical trials, test-validation sets, blah, blah
But doesn’t this lead to enormous overheads?
Answer: yes, but there are shortcuts
But if you take these shortcuts then don’t you run the risk of running into costly failures when you finally run the clinical trials?
It goes on….

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ML Embeddings and the Neuronal Code

I had the opportunity to talk recently with a relatively advanced researcher in machine learning methods. The conversation turned briefly to the study of embeddings when he mentioned that most of his work involves things that can be embedded in Euclidean space. Since I’ve been spending a bit of time thinking about embeddings recently, I asked him some questions to get the official ML take on the subject. I was resonably gratified to learn that – although most ML engineers don’t think much about embeddings – the research on this topic considers the embedding to be tightly bound to the network architecture. It is not possible to study abstract embeddings, divorced from applications. I fully agree with this point-of-view.

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