Monthly Archives: January 2023

Some ponderings on generalisability

Now that machine learning has managed to get its proverbial fingers into just about every pie, people have started to worry about the generalisability of methods used. There are a few reasons for these concerns, but a prominent one is that the pressure and publication biases that have led to reproducibility issues in the past are also very present in ML-based science.

The Center for Statistics and Machine Learning at Princeton University hosted a workshop last July highlighting the scale of this problem. Alongside this, they released a running list of papers highlighting reproducibility issues in ML-based science. Included on this list are 20 papers highlighting errors from 17 distinct fields, collectively affecting a whopping 329 papers.

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Happy 10th Birthday, Blopig!

OPIG recently celebrated its 20th year; and on 10 January 2023 I gave a talk just a day before the 10th anniversary of BLOPIG’s first blog post. It’s worth reflecting on what’s stayed the same and what’s changed since then.

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SAbBox in 2023: ImmuneBuilder and more!

For several years now, we have distributed the SAbDab database and SAbPred tools as a virtual machine, SAbBox, via Oxford University Innovation. This virtual machine allows a user to utilise the tools and database locally, allowing for high-throughput analysis and keeping confidential data within a local network. Initially distributed under a commercial licence, the platform proved popular and, in 2020, we introduced a free academic licence to enable our academic colleagues to use our tools and database locally.

Following requests from users, in 2021 we released a new version of the platform packaged as a Singularity container. This included all of the features of SAbBox, allowing Linux users to take advantage of the near bare-metal performance of Singularity when running SAbPred tools. Over the past year, we have made lots of improvements to both SAbBox platforms, and have more work planned for the coming year. I’ll briefly outline these developments below.

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The Boltzmann Distribution and Gender Stereotypes

Journalist Caitlin Moran recently tweeted the following:

“I feel like every day now, I read/hear something saying “We don’t talk about what’s POSITIVE about masculinity; what’s GOOD about men and boys.” So: what IS the best stuff about boys, and men? Honest, celebratory question.”

What followed was a collection of replies acknowledging and celebrating various traits seen typically as ‘male’, including certain activities, such as knowing about sports or cars, or a desire to do DIY type work, and characteristics such as physical strength, no-nonsense attitudes and a ‘less complicated’ style of friendship between men.

Whilst I condone Moran’s efforts to turn recent discussions surrounding masculinity on their head and frame it in a positive light, to me the the responses offered and discussion that followed felt somewhat stifling. I am biologically male and identify as male, but do not feel like I personally adhere to most of these stereotypes. I am not physically strong, I know very little about cars and sports, and find there be just as much nuance and drama in male-male friendships as there is in friendships between other genders. 

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Three months in industry and returning to my PhD

Being in my third year of my DPhil, I decided that I should try to see what the world of industry looks like. Thankfully, I was lucky enough to be able to complete an industrial internship at Exscientia here in Oxford where I spent most of my time on scientific software engineering. I expected this to not be too different from what my work looks like here at OPIG, but quickly came to realise that this is not the case. What followed were three months of building a software package, getting to know all the new people around me, and getting used to all the new tools and infrastructure. Below are a few things that I am very happy to take back with me. 

Read more: Three months in industry and returning to my PhD

A PhD can often be very solitary work. You are the expert in your project, and also have the highest stake in your project. At times, the freedom of what to explore next this affords is fantastic, but can make things difficult when problems arise. In industry, projects are a lot more collaborative. Your work direction will be aligned heavily with company needs, and depending on company size there might be specialised teams to support you in specific aspects of the project. 

Emphasis placed on code quality is also a stark difference. Internal software written for company use has to be readable and well-documented. The codebase must also be standardised to maintain consistency. This will make life for newcomers easy and ensures that if the author of some software leaves the company the next person can easily take on the task of maintaining their code. Here, academia is catching up. Scientific software engineering is becoming more focused on maintainability (one of the core values of the SABS programme), but sadly Github is still full of legacy code that was written in ways that make maintaining the code difficult after the author stops being involved with it.

Lastly, on a more personal note, it was also fantastic to be surrounded by people in a team who work with the same techniques as me. In my PhD, I am one of two people at OPIG regularly using molecular dynamics simulations but I also spend a lot of my time working in the Biochemistry Department with the Higgins Group which is an experimental structural biology group. This being the case, my internship has been a fantastic way of picking up some additional techniques from people who are already familiar with them. I would highly recommend giving yourself the opportunity to do this if possible, either via something like an industrial internship, or a research visit to a collaborating academic group. 

The past three months have been invaluable. They have given me the opportunity to see what industry is like and given me experience with new skills that I can take back to my PhD. Best of all, I got to meet a fantastic team who were always ready to take time out of their days to help and who made the time I spent at Exscientia as fun as it was!