iiinova — where your digital self keeps evolving

Ramith Hettiarachchi @ramith.fyi · 26/09/2026

Being gpu poor can be a good thing.. u come up with way efficient ways to train models…

Reposted by Ramith Hettiarachchi

RCSB Protein Data Bank @rcsbpdb.bsky.social · 28/08/2026

wwPDB Remediation of Metal-containing PDB Entries and CCDs Improved accuracy and annotation metal-containing PDB Entries and CCDs are now available in remediated PDB data.

rcsb.org

Remediation of Metal-containing PDB Entries and CCDs

Improved accuracy and annotation metal-containing PDB Entries and CCDs are now available in remediated PDB data.

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Ramith Hettiarachchi @ramith.fyi · 25/08/2026

need a quick web tool to understand protein - ligand interactions? try this out pli.ramith.fyi it runs ProLIF in the browser and visualizes the interactions if you want to explore plinder specifically try: --> plinder.ramith.fyi

pli.ramith.fyi

Weaver · Molecular interaction explorer

Weaver: a private, browser-native molecular interaction explorer

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Ramith Hettiarachchi @ramith.fyi · 07/08/2026

I used to have a lot attention to detail before llms 😅 feel like gradually its declining 🤦‍♂️

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Ramith Hettiarachchi @ramith.fyi · 27/07/2026

Does AF2 structure module transport the zero initialized frames to the endpoints? Weight tied 8 blocks or so 🤔 Feels like a generative model to some degree

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Ramith Hettiarachchi @ramith.fyi · 25/07/2026

interesting looking one alphafold.ebi.ac.uk/entry/AF-A0A...

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Ramith Hettiarachchi @ramith.fyi · 22/07/2026

ChatGPT voice mode is really good. Was having several convos about some papers in the literature, asked it to clone the repo etc and asked questions..

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Ramith Hettiarachchi @ramith.fyi · 19/07/2026

been building an architecture explainer/explorer tool where you can go in varying depth of abstraction to understand: - started with the genie3 (in progress), then go towards AF2 Underneath, it's a compiler for turning model architecture descriptions into interactive diagrams scope.new.ramith.fyi

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Ramith Hettiarachchi @ramith.fyi · 18/07/2026

Living in the present moment is such a challenge 😆

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Ramith Hettiarachchi @ramith.fyi · 18/07/2026

took me 4-5 days to recover from jetlag 🤦‍♂️

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Reposted by Ramith Hettiarachchi

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 16/07/2026

@wheelerlab.org is talking about his effort to build a resource for protein dynamics (PDB for MD). MDRepo is a repository to store simulation data. This is really needed to push the needle in design, function and more. Please help make it successful by sharing your MD data. #ismb2026 🌐 mdrepo.org

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Ramith Hettiarachchi @ramith.fyi · 13/07/2026

Interesting how ai generated music is easy to identify.. has something to do with the lyrics that sound like an essay and the frequency modulations of the voice🤔

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Ramith Hettiarachchi @ramith.fyi · 13/07/2026

is there a repo where esmfold is optimized for somewhat fast folding?

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Ramith Hettiarachchi @ramith.fyi · 11/07/2026

Glad to have worked with this amazing team in organizing the GenBio workshop! ❤️ (There’s lot more who helped behind the scenes and couldn’t join in this picture) GenBio has been a great venue to bring researchers and foster very interesting convos.. wish I had more time to talk to even more ppl 😆

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Ramith Hettiarachchi @ramith.fyi · 11/07/2026

love scientists who have a decent EQ

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Ramith Hettiarachchi @ramith.fyi · 07/07/2026

Claude generated slides kinda give me the ick.. Slides are meant to be simple, somewhat imperfect and human

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Ramith Hettiarachchi @ramith.fyi · 07/07/2026

Registration line 😅 even after two days of registration.. ml conferences maybe reaching a breaking point 😆 i guess it makes more sense to have more decentralized events

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Ramith Hettiarachchi @ramith.fyi · 06/07/2026

Is there a simple way to add bookmarked posters (icml) to the phone’s calendar 🧐

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Ramith Hettiarachchi @ramith.fyi · 05/07/2026

First impression of SK: everything has a touch of cuteness ^_^

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Ramith Hettiarachchi @ramith.fyi · 02/07/2026

So ESMFold2 uses 3DRoPE to enforce a geometry like pairbias (without the mem complexity of the standard pairbias) in its atom transformer… Wonder if the next stage, token transformer could’ve survived a similar approach (rather than the ln proj of z)

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Ramith Hettiarachchi @ramith.fyi · 20/05/2026

Glad to have contributed to this study on the computational side.. 😃 Thanks to implosion carving, we can now build devices that operate in the visible wavelength regime for classification tasks. Machine learning driven physical device design is pretty exciting.. news.mit.edu/2026/powerfu...

news.mit.edu

Powerful shrinking technique could enable devices that compute with light

MIT researchers made 3D devices with nanoscale features that can perform optical computing tasks using visible light. They developed a technique that creates vacancies throughout a hydrogel, then shri...

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Reposted by Ramith Hettiarachchi

Mohammed AlQuraishi @moalquraishi.bsky.social · 08/05/2026

Equivariance is dead! 😢 Or is it? 😈 Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa. It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇

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Ramith Hettiarachchi @ramith.fyi · 24/04/2026

claude is good at making posters through html.. feels like doing everything programmically is better 😅 used to love editing stuff on illustrator

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Ramith Hettiarachchi @ramith.fyi · 16/04/2026

La proteina’s autoencoder can be thought of as a inverse folder to some degree 🤔 Wonder if just giving Ca, along with a random partial latent acts as a inverse folder (true we get the all atom structure as well)

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Ramith Hettiarachchi @ramith.fyi · 16/04/2026

Consider submitting your work to the GenBio workshop at ICML 2026! We have an amazing set of speakers whose work spans generative and agentic AI. Deadline: May 1, 2026 genbio-workshop.github.io/2026/

genbio-workshop.github.io

GenBio ICML Workshop 2026

The 2026 workshop on Generative and Agentic AI for Biology at ICML 2026, Seoul, South Korea.

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Ramith Hettiarachchi @ramith.fyi · 08/04/2026

noticing that backbone design models trained on AFDB 588K, when sampled through ODE results in poor designability (~25%). But through a proper noise schedule in SDE it goes to 90% (as reported in lit.) this felt counterintuitive, wonder if the reason is, AFDB being just 42% designable to begin with

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Ramith Hettiarachchi @ramith.fyi · 08/04/2026

this [1] is nice, easier than having to type the passphrase of a ssh key all the time.. made a simpler guide [2] inspired by it [1] - gist.github.com/arianvp/5f59... [2] - gist.github.com/ramithuh/a7b...

gist.github.com

Native Secure Enclaved backed ssh keys on MacOS

Native Secure Enclaved backed ssh keys on MacOS . GitHub Gist: instantly share code, notes, and snippets.

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Ramith Hettiarachchi @ramith.fyi · 08/04/2026

In 10 years we might have an EEG headset that decodes thoughts, and routes to claude 😆 Would be a true brain computer interface 😅

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Ramith Hettiarachchi @ramith.fyi · 15/03/2026

training a flow matching model for protein backbone design (N, Ca, C) intra residue geometry is somewhat easy to learn, but inter-residue (peptide bond length, Ca-C-N and C-N-Ca angles) doesn't consistently match ideal stereochemical params [1] [1] www.ebi.ac.uk/thornton-srv...

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Ramith Hettiarachchi @ramith.fyi · 14/03/2026

it always amazes me that after a mac update there's more free storage than what was before updating

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Ramith Hettiarachchi @ramith.fyi · 10/03/2026

sometimes asking claude to start an agent to figure out a bug is more effective than asking claude directly. The reason being, the prompt i give is not as descriptive as the prompt it generates for the agent

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Ramith Hettiarachchi @ramith.fyi · 10/03/2026

its always satisfying to figure out what causes a DDP training job to get suck

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Ramith Hettiarachchi @ramith.fyi · 06/03/2026

its interesting how MSA is very important for protein structure prediction to extract co-evolution signals, but in the small molecule design/conformer generation scenarios with the scale we are working, the model can "learn physics"

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Ramith Hettiarachchi @ramith.fyi · 04/03/2026

im reorganizing one of my old repo coded in JAX, I'm starting to question whether in the age of claude code, how important is knowing syntax, etc.. 😅 feels like ideas matter more than the implementation at this time, where coding is straightforward if you ask the right fundemental questions

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Ramith Hettiarachchi @ramith.fyi · 26/02/2026

today i learnt that you can filter runs on @weightsbiases.bsky.social using the git commit id

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Ramith Hettiarachchi @ramith.fyi · 18/02/2026

starting to love the @marimo.io notebook's reactive cell execution. all the nodes in the DAG are on the same page!

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Ramith Hettiarachchi @ramith.fyi · 11/02/2026

ran 3 python codes, all 3 were using the same cpu core while 19 were free 🤔 i thought the os is supposed to handle this

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Reposted by Ramith Hettiarachchi

Yunha Hwang @microyunha.bsky.social · 04/02/2026

First, @tattabio.bsky.social is now on Bluesky!💙 and second, we launched mult-sequence CoSearch on SeqHub!

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Ramith Hettiarachchi @ramith.fyi · 03/02/2026

@marimo.io's hover tooltips showing function signatures & docs is nice

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Ramith Hettiarachchi @ramith.fyi · 26/01/2026

building a website through @typst.app is kinda straightforward.. was trying out this template: github.com/vsheg/tufted, forum.typst.app/t/tufted-web... for eg: Below you can see an example post from their template: new.ramith.fyi/posts/2025-1...

Screenshot of the Typst web application interface showing a split-screen view of a project titled "typst-website." The left panel displays a file directory with a "posts" folder expanded, revealing various dated entries. The center panel contains a code editor with Typst markup for a document titled "The Normal Distribution," including text, mathematical syntax for the probability density function, and code for generating a diagram. The right panel shows the live preview of the rendered document, featuring formatted text, the mathematical formula clearly typeset, and a blue histogram chart illustrating the distribution. The path bar at the top indicates the file location: Ramith > typst-website > content > posts > 2025-10-30-normal-distribution > index.typ

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Ramith Hettiarachchi @ramith.fyi · 09/01/2026

does flash attention variants support arbitrary attention biases 🤔

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