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Ramith Hettiarachchi

@ramith.fyi
776 followers 1K following 368 posts

PhD Student @CMUPittCompBio.bsky.social / @SCSatCMU.bsky.social Interested in ML for science/Compuational drug discovery/AI-assisted scientific discovery 🤞 from 🇱🇰🫶 new.ramith.fyi

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Ramith Hettiarachchi @ramith.fyi · 26/09/2026
www.youtube.com/watch?v=WdIf...
youtube.com
Waking up a thankful doggo having a nightmare.
YouTube video by Plastic Ivory
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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…
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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 · 28/06/2026
damn Grant is an incredible teacher..
youtu.be
Designing Math ft. Grant Sanderson (3Blue1Brown) I Config 2026
YouTube video by Figma
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Ramith Hettiarachchi @ramith.fyi · 07/06/2026
<3
youtu.be
Nimsara Vs Janith | Saragaye ( සරාගයේ ) | The Battles | The Voice Teens Sri Lanka S3
YouTube video by The Voice Sri Lanka
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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 · 12/04/2026
❤️
youtu.be
Janith Kalhara |Suragana Kirilliye(සුරඟන කිරිල්ලියේ) |Blind Auditions | The Voice Teens Sri Lanka S3
YouTube video by The Voice Sri Lanka
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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 · 28/03/2026
rossjtaylor.com/blog/qk-norm...
rossjtaylor.com
Notes on the Membrane - Ross Taylor
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Ramith Hettiarachchi @ramith.fyi · 23/03/2026
youtu.be/e1mOmdykmwI
youtu.be
Elliot James Reay - I Think They Call This Love (Official Music Video)
YouTube video by Elliot James Reay
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Ramith Hettiarachchi @ramith.fyi · 19/03/2026
it always amazes me..
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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...
intra residue paramsinter residue params
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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 · 03/03/2026
Scared to use less popular vscode extentions etc after reading this
socket.dev
Unauthorized AI Agent Execution Code Published to OpenVSX in...
OpenVSX releases of Aqua Trivy 1.8.12 and 1.8.13 contained injected natural-language prompts that abuse local AI coding agents for system inspection a...
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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 · 02/02/2026
I like how @anthropic.com is doing research into the downsides of AI use.. so that we can improve how we interact/get help www.anthropic.com/research/AI-...
anthropic.com
How AI assistance impacts the formation of coding skills
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
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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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