Why do 'frontier' labs train the best models? I think its because training deep learning models is less like science/engineering, and more like cooking. It takes some time to develop the intuitions around learning dynamics of big models.

The results are in: top codes in Stanford #RNA 3D Folding @kaggle.com competition are competitive with CASP16-leading humans Vfold, beat AlphaFold 3. Top team’s trick was template-based modeling, not #DeepLearning. Congrats: john, odat, Eigen, + all 1706 participants! www.kaggle.com/competitions...

🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE. Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.

Genome language models can generate new, high-fitness bacteriophages! @samuelhking.bsky.social @claudiadriscoll.bsky.social @david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.1...

Many of the most complex and useful functions in biology emerge at the scale of whole genomes. Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

very cool work and a milestone in synthetic biology. how impressive are the new phage genomes? with generative bioML, i'm always looking at how similar the generated sequences are to known sequences. let's take a look

You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉 Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫

The 3D structure of biomolecules are nature's 'thinking tokens' enroute to the output that we actually truly want to understand: Function. (Slide from Denny Zhou's Stanford talk on LLM Reasoning)

We have restarted our global Nucleic Acid Strcuture webinar series to bring the expiremental and computational communities together to discuss new developments in the field. Join us this Thursday for the next webinar. Sign up to our mailing list here: groups.google.com/g/casp-rna-sig

Scaling laws for BioML and wet lab data will eventually work out in the right setting! After all, language data for LLMs was acquired by the largest wet lab experiment ever conducted: Human civilisation 🤯

(1/7) Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3) [https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)

📢 Submissions for MLSB 2025 are officially open! We invite researchers to submit their work on the intersection of AI and structural biology. 🗓️ Deadline: September 26, 2025 🔗 More info: cmt3.research.microsoft.com/MLSB2025

RosettaFold 3 is here! 🧬🚀 AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release! Congratulations @simonmathis.bsky.social and team!!! ❤️ bioRxiv preprint: www.biorxiv.org/content/10.1...

Really insightful post and responses - this is why I keep coming back to science social media!

🧬 Protein designers: we keep saying we're getting really good at making static, rock-like proteins... Introducing Dynamic MPNN - our first step towards truly multi-state and 'programmable' protein design! Great collaboration led by Alex Abrudan and Sebastian Pujalte!

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

Coming up this weekend, Eternacon will feature presentations about fellow #citsci platform @zooniverse.bsky.social and how participants of both Zooniverse and Eterna have created #machinelearning tools for projects. @noirlabastro.bsky.social Register for free at eternagame.org/eternacon/2025

Are we hitting a wall with scaling molecular foundation models? Some thoughts on what I think is one of the most interesting open Qs atm: chaitjo.substack.com/p/transfer-l...

How does a cell know when it’s been damaged? A molecular alarm, set off by mutated RNA and colliding ribosomes, signals danger. @dsamorod.bsky.social reports: www.quantamagazine.org/rna-is-the-c...

We are looking to recruit a tenure track group leader in the field of Chemical/Synthetic Biology (in the broadest sense) to lead a research program within the Division of Protein & Nucleic Acid Chemistry ( www.jobs.ac.uk/job/DNW809/r... ) at the MRC Laboratory of Molecular Biology (LMB).

Highly collaborative efforts that involved 6 lab members and the labs of @yiliangding.bsky.social and @rdaslab.bsky.social. We uncovered a telomerase dimer and its potential role in telomere maintenance.

Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year. Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology” More on the future of MLSB soon…

Needing a permanent doi was a forcing function to revisit this article on Transformers and Graph Neural Networks: arxiv.org/abs/2506.22084 This is (very) old news, so what's new?

This was posed by a VC (@dreidco.bsky.social ) on LinkedIn. Just a thought: Maybe Boltz-2 is also a moment similar to GPT-3 where a sizeable part of the community moves on from academic publishing and to the world of capabilities, tech reports, and shipping models

Check out this post from @ffabffrasca.bsky.social and the GLOW reading group on the future of graph learning! I’ve also contributed and my main take is - its actually working and its an exciting moment to work on applications! open.substack.com/pub/glowread...

Interested in a postdoc position combining computational protein design and molecular simulation? There is an open position in my group at the MRC-LMB in Cambridge, UK. www.nature.com/naturecareer... Feel free to message me with any questions.

Have you ever been frustrated by how hard it is to tinker with AlphaFold 3? Here's a (hopefully) simple repo to instal locally on laptop/single-GPU and a handy notebook to play around with! github.com/chaitjo/alph...

After a long hiatus, I've started blogging again! My first post was a difficult one to write, because I don't want to keep repeating what's already in papers. chaitjo.substack.com/p/transforme...

How did life on Earth begin? 🌍🧬 New #LMBResearch from Phil Holliger’s group, including James Attwater (now @uclchemistry.bsky.social‬‬ @uclnews.bsky.social) shows how pH-freeze-thaw cycles enables RNA self-replication, overcoming a key evolutionary hurdle.‬ Read more: www.ucl.ac.uk/news/2025/ma...

New paper from my group rdcu.be/eoaRr "Trinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozyme" in Nature Chemistry — great collaboration with attwaterlab.uk.

Sharing a surprising result on AI molecule generation with Transformers: All-atom DiT with minimal molecular inductive bias is on par with SOTA equivariant diffusion (SemlaFlow, a very strong and optimized model) Scaling pure Transformers can alleviate explicit bond prediction!

What is the status of nucleic acid structure prediction? Our analysis of CASP16 (doi.org/10.1101/2025...) reveals human expertise is still necessary for the most accurate prediction, but accuracy still heavily relies on templates; having seen a similar structure already.

Happy to be a small part of this humongous effort by the inimitable Srijit!

Equivariance is dead - long live equivariance? Scaling pure Transformers is the future of molecular generative models? I think its a lot more nuanced -- I tried to give some perspectives in my spotlight talk at #ICLR2025 AI4Mat Workshop last week Full video here: youtu.be/NiY4NLzemnU?...

Equivariance is dead - long live equivariance? Scaling pure Transformers is the future of molecular generative models? I think its a lot more nuanced -- I tried to give some perspectives in my spotlight talk at #ICLR2025 AI4Mat Workshop last week Full video here: youtu.be/NiY4NLzemnU?...

Thanks to everyone involved in the AI for Nucleic Acids Workshop at #ICLR2025! And oh my god - the panel was a 🌶️🌶️🌶️ finish to an exciting day of science, discussions, and community! @pranam.bsky.social @kishwar.bsky.social @bunnech.bsky.social and many others!

A reminder that @aithyra.bsky.social has an open call for starting PIs. We offer some of the best conditions in Europe rivalling MP and ETHZ www.oeaw.ac.at/aithyra/news...

Really nice resource from @delalamo.xyz !! Wanna mention the "AdK test" we're noticing newer DL methods fall short on: many proteins (like AdK) that have apo/holo conf change sample both the apo/holo state even without ligand bound. But w/o ligand bound, they *are mainly in the apo state*

Next Tues (4/29) at **4:30PM** ET, we will have @ginaelnesr.bsky.social @hkws.bsky.social present "Learning millisecond protein dynamics from what is missing in NMR spectra" Paper: biorxiv.org/content/10.1... Sign up on our website for zoom links!

Here are some recommendations for first timers in Singapore for #ICLR2025 that I’ve been sharing with friends! 🇸🇬 So excited that the ML world will gather in Singapore - And hoping to help people have a great time here! 🤗

I'll be at #ICLR2025 🇸🇬 in Singapore next week: - gRNAde - 🌟 Spotlight poster no.616 - 25th, Fri 10am - All-atom Diffusion Transformer - 🌟 Spotlight talk at AI4Mat workshop - 28th, Sun 3.30pm - 28th, Sun all day - Organizing AI for Nucleic Acids workshop See you soon in Sg! 👋

This has been a long journey, but it's now out in final form. @kjamali.bsky.social academic.oup.com/bioinformati...

RNA 3D structure prediction is within reach - the experts see a path to get there based on scaling laws of experimental dataset collection and big Transformers nets - but we need GPUs to get there! 🙏 x.com/RDasLab/stat...

Sharing slides for All-atom Diffusion Transformers - briefly summarises the big ideas and key takeaways Link - www.chaitjo.com/publication/...

Sharing slides for All-atom Diffusion Transformers - briefly summarises the big ideas and key takeaways Link - www.chaitjo.com/publication/...

Don’t miss the 2025 César Milstein Lecture, by David Pellman from the Dana-Farber Cancer Institute and Harvard University. Join us at 10am (BST) on Thu 24th April to learn about “Mechanisms driving the rapid evolution of genomes” More details: www2.mrc-lmb.cam.ac.uk/news-and-eve... #LMBSeminar

Excited to be a keynote speaker at the Netherlands Society on Biomolecule Modelling annual meeting tomorrow! I'll be speaking about All Atom Diffusion Transformers for the first time publicly! Thank you @erikjbekkers.bsky.social for the invitation 🙏 www.nsbm.nl

This was an amazing podcast -- I'd heard David Baker talk a lot about the science before at talks/other podcasts -- But here he dives into the science of science, or the philosophy of how the @uwproteindesign.bsky.social is organized as a community for doing amazing science!

Floored by the interest in the All-atom Diffusion Transformers codebase already: github.com/facebookrese... I've fixed a lot of small issues and tested on two different GPU clusters to ensure everything should now work out of the box. PS. lightning-hydra template makes for very modular code :)