Author Archives: Hew Phipps

Building a “Second Brain” – A Functional Knowledge Stack with Obsidian

Whilst I always enjoy the acquisition of knowledge, I’ve always struggled with depositing it usefully. From pen and paper notes with a 20 colour theme which lost value with each additional colour, to OneNote or iPad GoodNotes based emulations of pen and paper, it’s been a constant quest for the optimal note taking schema. Personally there are 3 key objectives I need my note taking to achieve:

  1. It must be digitally compatible and accessible from any device.
  2. It must comfortably handle math and images.
  3. It must be something I look forward to – the software needs to be aesthetically clean, lightweight with none of the chunkiness of Microsoft apps, and highly customisable.

For me the solution to this was Obsidian, the perhaps more cultified sibling to Notion. Obsidian is a note taking application that uses markdown with a surprising amount flexibility, including the ability to partner it with an LLM which I’ll explore in this blog, alongside my vault organisation do or dies, and favourite customisations.

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Getting In the Flow – How to Flow (Match)

Introduction

In the world of computational structural biology you might have heard of diffusion models as the current big thing in generative modelling. Diffusion models are great because primarily they look cool when you visualise the denoising process to generate a protein structure (checkout RFdiffusion Colab notebook), but also because they are state of the art at diverse and designable protein backbone structure generation.

Originally emerging from computer vision, a lot of work has been built up around their application to macromolecules – especially exciting is their harmonious union with geometric deep learning in the case of SE(3) equivariance (see FrameDiff). I don’t know about you but I get particularly excited about geometric deep learning, mostly because it involves objectively dope words like “manifold” and “Riemannian”, better yet “Riemannian manifolds” – woah! (see Bronstein’s geometric deep learning for more fun vocabulary to add to your vernacular- like “geodesic”, Geometric Deep Learning).

But we’re getting side tracked. Diffusion is a square to rectangle case of score-based generative models with the clause that diffusion refers explicitly to the learning of a time-dependent score function that is typically learned via a denoising process. Checkout Jakub Tomczak’s blog for more on diffusion and score-based generative models. Flow matching, although technically different to score-based generative models, also makes use of transformations to gaussian but is generally faster and not constrained to discrete time steps (or even Gaussian priors). So the big question is, how does one flow match?

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Le Tour de Farce v12.0

Bikes and pints across 5 pubs – what could be better (and what could go wrong). The year is 2025 and the date 06.06.25. Starting from the Stats department the customary picture was taken before the horn blown and a flood of ~30 structural biologists was unleashed onto the streets of Oxford to raid and plunder. Despite being the new kid I think Fergus will be proud to see my accurate version controlling unlike past more experienced members of the group, and that this reference doesn’t seem like copying his homework too much.

Of course even though it was June the weather was tumultuous. Having to make an educated guess on the probability of experiencing rain I took a Bayesian approach to calculate the posterior of rain occurring given the data of the entirety of British history which suggested that despite seeing sun on the BBC weather report that did not in anyway improve the likelihood of there being later rain. In light of this everyone came aptly dressed in waterproofs which turned out to be a smart choice after a later event of spontaneous beer spillage where a certain individual knocked his entire pint over Sophie and proceeded to say “at least you were wearing a raincoat”. This was a fantastic play by the newest member of the group who destroyed what little dignity (if any) he had so far amassed and simultaneously embroiled himself in the responsibility of this blog post. So to Charlotte who I know will be reading this (as I was warned!) perhaps this blog post will be an adequate first step to redemption.

And so the convoy departed towards our first stop, the Up in Arms (thanks Charlotte for the round). The inaugural table tennis tournament was held and it was great to see a real world application of the groups protein folding experience with Odysseus’s portable bike.

Next stop, the Victoria (thanks Matt for the round), before the 3.5 mile cycle to The Plough (I recommend going to the toilet before this after drinking units in the metric of pints).

Being far removed from our hunter gatherer past we settled down on the crisp summer grass with Oxford’s famous White Rabbit pizza delivered directly to the local meadow. I hadn’t grounded myself and connected to the earth like that in months (preferring to spend my days with my quadruple monitor workstation setup in the department) which combined with the beautiful settings of port meadow was making the trees look huggable. After scavenging 4 more pieces of pizza for a profit of 50% on my original contribution despite my intolerance to onions – whilst arguing that tolerance is a mental game aided by alcoholic bravery – we walked down the field to the river to reach our final destination – the idyllic medley looking over the Thames.

Reaching our last stop it dawned on me that despite proclaiming an ambitious target of 2 pints per pub I was sitting well below that at 3 pints total. It was clear desperate actions were needed to raise my average to stand up to any later scrutiny. Perhaps it was this subconscious desire to complete my self-assigned quest that at this last point of interest I executed the “swill Sophie” manoeuvre. Yet, despite my insistence that by getting through 2 pint glasses this was “technically” equivalent two my 2 pints per pub target, this did not stand up to the scrutiny of Charlotte.

After a month of wrangling with HPC molecular dynamics I’ve been getting more contact with the Slurm e-mail notification service than real human beings so it was refreshing to escape the GROMACS simulation that my brain has become and get to know the group better. Yet by the end of the night some of us (myself) couldn’t resist entering a tirade about how fractals and symmetry is the underlying representation of consciousness with the source being a strong “trust me bro”, and so it seemed liked a fitting time to put myself to bed.

Thanks to Eoin for organising!