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A short history of protein language models: AAIndex + onehot are ok LSTM/VAE are ok Transformers is all you need Scaling is all you need Multimodality is all you need What? 🤔 PLMs are biased towards certain taxa/folds Wee need ad hoc loss fx PLM has massive activations

hello beautiful people of twitter, I've decided to start sharing my notes from reading AI&Bio papers on substack <3 (essentially because reading and writing are great but sadly I am incapable of doing anything without a deadline🥲) open.substack.com/pub/lindsaytts…

The further a scientist moves away from the topic of their previous work, the fewer citations their new work will receive, according to an analysis of millions of scientific papers and patents published in nature. go.nature.com/3HdyflX

🚀 DeepSeek-R1-0528 is here! 🔹 Improved benchmark performance 🔹 Enhanced front-end capabilities 🔹 Reduced hallucinations 🔹 Supports JSON output & function calling ✅ Try it now: chat.deepseek.com 🔌 No change to API usage — docs here: api-docs.deepseek.com/guides/reasoni… 🔗

FoldBench: An All-atom Benchmark for Biomolecular Structure Prediction １．FoldBench presents the first unified all-atom benchmark spanning proteins, nucleic acids, ligands, and diverse molecular interactions. It enables systematic comparison of state-of-the-art structure

New #AlphaFold materials now live! Earlier this year, with Google DeepMind, we held the AlphaFold Education Summit to increase capacity and enable more researchers to use the #AlphaFold system and database. View the free course materials: ebi.ac.uk/training/mater… EMBL-EBI

📢 Introducing Biomni - the first general-purpose biomedical AI agent. Biomni is built on the first unified environment for biomedical agent with 150 tools, 59 databases, and 106 software packages and a generalist agent design with retrieval, planning, and code as action. This

Our recent paper was featured in Nature News! How wonderful to see helix-hairpin-helix motifs finally getting the attention they deserve 🧬 🎉 Check our out paper here: onlinelibrary.wiley.com/doi/full/10.10… Check out the Nature News story here: nature.com/articles/d4158…

Open PhD position! Would like to design protein robots using Nobel prize-winning protein design methods? Please apply and choose topic 12. ki.si/en/news/tender…

Trump: Just give me a list o all "woke-related" things that I have to cancel to make America great again. The white house 🥸: grep -Eo '\bhomo\w*' grants.txt > no_grants.txt

Good times to be a protein designer? 💵💰

90% of doing science is being open to new ideas.

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. I tried to give some nuanced and (hopefully) fresh takes on equivariance and geometry in molecular modelling.

Residue conservation and solvent accessibility are (almost) all you need for predicting mutational effects in proteins １．A simple model called RSALOR achieves performance on par with or better than most state-of-the-art tools in predicting the effects of mutations on proteins

Do protein language models store different structural elements in factorizable subnetworks? To find out, we masked out PLM weights to suppress performance on CATH subcategories or secondary structure elements while maintaining performance on other sequences or residues.

Let's overfit to the world to build a true world model 🤪 Welcome to the Era of Experience storage.googleapis.com/deepmind-media…

Antoher reason to use* ChimeraX instead of PyMOL 🔥 *unless uou're a company. Licenses: Single-User: $2k Six-User: $10k Unlimited-User: $20k Global (can be used at multiple sites): $50k rbvi.ucsf.edu/chimera/commer…

It feels like they're announcing a festival along with the headliners. Here is a personal list of researchers in AI-based protein science whose work I really admire, they’re incredibly creative! And a longer list of other colleagues working in the field x.com/miangoar/statu…