In our silly little day-to-day lives in over in stats, we forget how accustomed we all are to AI being used in many of the things we do. Going home for the holidays, though, I was reminded that the majority of people (at least, the majority of my family members) don’t actually make most of […]
Some time ago, I needed to find a way to computationally estimate conductance values for every protein frame from several molecular dynamics (MD) trajectories. In a previous post, I wrote about how to clean the resulting instant conductance timeseries from outliers. But, I never described how I generated these timeseries. In this post, I will […]
Recently, I have become quite interested in how countries have been shaping their national AI strategies or frameworks. Since the launch of ChatGPT, several concerns have been raised about AI safety and how such groundbreaking AI technologies could augment or adversely affect our daily lives. To address the public’s concerns and set standards and practices […]
Or: The best lies have a nugget of truth in them. Lucubration – The action or occupation of intensive study originally by candle or lamplight. Gaslighting – Psychological abuse in which a person or group causes someone to question their own sanity, memories, or perception. I was recently having a play with Google Bard. Bard, […]
figure making scripts. With these scripts I manage to produce figures that made people question what I had actually been doing with my time – but I promise this will be worth your time.
I have been using with dimensionality reducition techniques recently and I came across this paper by Moon et al. PHATE is a technique that represents high dimensional (ie biological) data in a way that aims to preserve connections over preserving distance and I knew I wanted to try this as soon as I saw it. Why should you care? PHATE in 3D is faster that t-SNE in 2D. It would almost be rude to not try it out.
Detecting atom clashes in protein structures can be useful in a number of scenarios. For example if you are just about to start some molecular dynamics simulation, or if you want to check that a structure generated by a deep learning model is reasonable. It is quite straightforward to code, but I get the feeling […]
As my turn to write a blog post has fallen a few days after April 1st, I decided I would write an April Fools’ Day-inspired post and ask everyone’s favourite chatbot to tell me some jokes. I asked ChatGPT to tell me a knock-knock joke, prompting it with various topics relevant to OPIG (including AI, […]
One of the most treasured group meeting institutions in OPIG is snackage. Each week, one group member is asked to bring in treats for our sometimes lengthy 16:30 meeting. However, as would be the case for any group of 25 or so people, there are various dietary requirements and preferences that can make this snack-quisition […]
When I started my PhD in late 2018, AI hadn’t really entered the field of de novo protein design yet – at least not in a big way. Rosetta’s approach of continually ranking new side chain rotamers on a fixed backbone was still the gold standard for the ‘structure-to-sequence’ problem. And of course before long […]